rs1637670

Variant names:

• chr7-34955463-A-G
• rs1637670
• NM_001366673.1:c.1180-96T>C

Variant summary

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

The NM_001366673.1(DPY19L1):​c.1180-96T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,478,772 control chromosomes in the GnomAD database, including 72,037 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 0.28 (6184 hom., cov: 31)
  • Exomes 𝑓: 0.31 (65853 hom.)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 6 publications found

Genes affected

DPY19L1 (HGNC:22205): (dpy-19 like C-mannosyltransferase 1) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000294671 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1	NM_001366673.1	c.1180-96T>C		intron_variant	Intron 11 of 21	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.961-96T>C		intron_variant	Intron 11 of 21		NP_056098.1
DPY19L1	XM_011515246.4	c.1093-96T>C		intron_variant	Intron 10 of 20		XP_011513548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2	c.1180-96T>C		intron_variant	Intron 11 of 21	5	NM_001366673.1	ENSP00000490722.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42633 AN: 151912 Hom.: 6172 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.311 AC: 412303 AN: 1326742 Hom.: 65853 AF XY: 0.309 AC XY: 203643 AN XY: 658570

African (AFR) AF: 0.214 AC: 6170 AN: 28892

American (AMR) AF: 0.234 AC: 7306 AN: 31210

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 8285 AN: 22932

East Asian (EAS) AF: 0.147 AC: 5345 AN: 36300

South Asian (SAS) AF: 0.236 AC: 17513 AN: 74128

European-Finnish (FIN) AF: 0.310 AC: 15184 AN: 48906

Middle Eastern (MID) AF: 0.313 AC: 1667 AN: 5324

European-Non Finnish (NFE) AF: 0.327 AC: 334376 AN: 1024100

Other (OTH) AF: 0.299 AC: 16457 AN: 54950

GnomAD4 genome AF: 0.281 AC: 42670 AN: 152030 Hom.: 6184 Cov.: 31 AF XY: 0.278 AC XY: 20646 AN XY: 74304

African (AFR) AF: 0.218 AC: 9047 AN: 41504

American (AMR) AF: 0.268 AC: 4100 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3470

East Asian (EAS) AF: 0.151 AC: 781 AN: 5176

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4822

European-Finnish (FIN) AF: 0.317 AC: 3344 AN: 10562

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22084 AN: 67896

Other (OTH) AF: 0.304 AC: 640 AN: 2108

Alfa AF: 0.292 Hom.: 1167

Bravo AF: 0.276

Asia WGS AF: 0.183 AC: 638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.82
PhyloP100		0.39
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: rs1637670; hg19: chr7-34995075;