5-101874544-G-A

Variant names:

• chr5-101874544-G-A
• rs7731840

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 0.827 in 152,078 control chromosomes in the GnomAD database, including 52,238 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 0.83 (52238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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: 0.827 AC: 125688 AN: 151960 Hom.: 52199 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.827 AC: 125778 AN: 152078 Hom.: 52238 Cov.: 31 AF XY: 0.831 AC XY: 61811 AN XY: 74340

African (AFR) AF: 0.823 AC: 34115 AN: 41458

American (AMR) AF: 0.853 AC: 13045 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5013 AN: 5168

South Asian (SAS) AF: 0.936 AC: 4520 AN: 4828

European-Finnish (FIN) AF: 0.845 AC: 8940 AN: 10582

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55075 AN: 67964

Other (OTH) AF: 0.810 AC: 1714 AN: 2116

Alfa AF: 0.816 Hom.: 14215

Bravo AF: 0.827

Asia WGS AF: 0.943 AC: 3275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7731840; hg19: chr5-101210248;