19-41137939-T-C

Variant names:

• chr19-41137939-T-C
• rs1631931
• ENST00000775808.1:n.274-515A>G

Variant summary

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

The ENST00000775808.1(ENSG00000301056):​n.274-515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,092 control chromosomes in the GnomAD database, including 52,027 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 0.82 (52027 hom., cov: 31)
• Consequence: ENSG00000301056 ENST00000775808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

Genes affected

ENSG00000301056 (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 (AMR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904790	XM_047439802.1	c.185-515A>G		intron_variant	Intron 2 of 2		XP_047295758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301056	ENST00000775808.1	n.274-515A>G		intron_variant	Intron 1 of 3
ENSG00000301056	ENST00000775809.1	n.396-515A>G		intron_variant	Intron 2 of 4
ENSG00000301056	ENST00000775810.1	n.201-515A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124979 AN: 151974 Hom.: 51983 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.822 AC: 125080 AN: 152092 Hom.: 52027 Cov.: 31 AF XY: 0.827 AC XY: 61496 AN XY: 74358

African (AFR) AF: 0.690 AC: 28599 AN: 41464

American (AMR) AF: 0.885 AC: 13523 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2919 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4487 AN: 5154

South Asian (SAS) AF: 0.858 AC: 4132 AN: 4818

European-Finnish (FIN) AF: 0.905 AC: 9595 AN: 10608

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59063 AN: 67992

Other (OTH) AF: 0.843 AC: 1780 AN: 2112

Alfa AF: 0.850 Hom.: 14038

Bravo AF: 0.813

Asia WGS AF: 0.883 AC: 3070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1631931; hg19: chr19-41643844;