rs4072910

Variant names:

• chr19-8579147-G-C
• rs4072910

Your query was ambiguous. Multiple possible variants found:

• chr19-8579147-G-C
• chr19-8579147-G-T

Variant summary

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

The variant allele was found at a frequency of 0.56 in 151,962 control chromosomes in the GnomAD database, including 24,713 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 0.56 (24713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85043 AN: 151844 Hom.: 24671 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.560 AC: 85137 AN: 151962 Hom.: 24713 Cov.: 32 AF XY: 0.567 AC XY: 42083 AN XY: 74264

African (AFR) AF: 0.692 AC: 28683 AN: 41476

American (AMR) AF: 0.600 AC: 9148 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3889 AN: 5158

South Asian (SAS) AF: 0.520 AC: 2504 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5944 AN: 10552

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31182 AN: 67940

Other (OTH) AF: 0.551 AC: 1163 AN: 2112

Alfa AF: 0.474 Hom.: 9287

Bravo AF: 0.571

Asia WGS AF: 0.667 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.34
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4072910; hg19: chr19-8644031;