rs741441

Variant names:

• chr19-32408168-G-A
• rs741441
• NM_001172774.2:c.-37-49G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-32408168-G-A
• chr19-32408168-G-C
• chr19-32408168-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001172774.2(DPY19L3):​c.-37-49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 881,448 control chromosomes in the GnomAD database, including 98,648 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (13670 hom., cov: 31)
  • Exomes 𝑓: 0.46 (84978 hom.)
• Consequence: DPY19L3 NM_001172774.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 12 publications found

Genes affected

DPY19L3 (HGNC:27120): (dpy-19 like C-mannosyltransferase 3) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Predicted to be integral component of membrane. Predicted to be active in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172774.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L3	NM_001172774.2	MANE Select	c.-37-49G>A		intron	N/A	NP_001166245.1	Q6ZPD9-1
	DPY19L3	NM_207325.3		c.-37-49G>A		intron	N/A	NP_997208.2	Q6ZPD9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L3	ENST00000392250.7	TSL:5 MANE Select	c.-37-49G>A		intron	N/A	ENSP00000376081.2	Q6ZPD9-1
	DPY19L3	ENST00000586427.1	TSL:1	c.-37-49G>A		intron	N/A	ENSP00000466062.1	K7ELG1
	DPY19L3	ENST00000587077.6	TSL:1	c.-37-49G>A		intron	N/A	ENSP00000465995.1	Q8N6Q4

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59432 AN: 151882 Hom.: 13673 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.465 AC: 339115 AN: 729448 Hom.: 84978 Cov.: 10 AF XY: 0.463 AC XY: 178404 AN XY: 385696

African (AFR) AF: 0.163 AC: 2994 AN: 18348

American (AMR) AF: 0.269 AC: 9123 AN: 33884

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 9352 AN: 18914

East Asian (EAS) AF: 0.143 AC: 5156 AN: 36014

South Asian (SAS) AF: 0.318 AC: 20301 AN: 63920

European-Finnish (FIN) AF: 0.512 AC: 26427 AN: 51598

Middle Eastern (MID) AF: 0.426 AC: 1111 AN: 2606

European-Non Finnish (NFE) AF: 0.531 AC: 248773 AN: 468542

Other (OTH) AF: 0.446 AC: 15878 AN: 35622

GnomAD4 genome AF: 0.391 AC: 59421 AN: 152000 Hom.: 13670 Cov.: 31 AF XY: 0.389 AC XY: 28905 AN XY: 74258

African (AFR) AF: 0.169 AC: 7022 AN: 41500

American (AMR) AF: 0.345 AC: 5266 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3472

East Asian (EAS) AF: 0.180 AC: 926 AN: 5152

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4812

European-Finnish (FIN) AF: 0.502 AC: 5289 AN: 10540

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36144 AN: 67940

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.487 Hom.: 11186

Bravo AF: 0.369

Asia WGS AF: 0.235 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs741441; hg19: chr19-32899074; COSMIC: COSV60477358; COSMIC: COSV60477358;