19-41167943-G-T

Variant names:

• chr19-41167943-G-T
• rs8105815
• XM_047439802.1:c.184+8016C>A

Variant summary

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

The ENST00000775808.1(ENSG00000301056):​n.273+8016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,028 control chromosomes in the GnomAD database, including 3,560 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 0.18 (3560 hom., cov: 31)
• Consequence: ENSG00000301056 ENST00000775808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 11 publications found

Genes affected

LOC124904790 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775808.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301056	ENST00000775808.1		n.273+8016C>A		intron	N/A
	ENSG00000301056	ENST00000775809.1		n.395+1167C>A		intron	N/A
	ENSG00000301056	ENST00000775810.1		n.200+8016C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26583 AN: 151910 Hom.: 3542 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26640 AN: 152028 Hom.: 3560 Cov.: 31 AF XY: 0.173 AC XY: 12831 AN XY: 74328

African (AFR) AF: 0.360 AC: 14899 AN: 41428

American (AMR) AF: 0.221 AC: 3363 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.0790 AC: 409 AN: 5174

South Asian (SAS) AF: 0.109 AC: 525 AN: 4822

European-Finnish (FIN) AF: 0.0555 AC: 588 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0927 AC: 6305 AN: 67998

Other (OTH) AF: 0.162 AC: 340 AN: 2104

Alfa AF: 0.119 Hom.: 6801

Bravo AF: 0.200

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.37
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8105815;

hg19: chr19-41673848;