chr5-71715685-T-C

Variant names:

• chr5-71715685-T-C
• rs4703647

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 0.615 in 151,896 control chromosomes in the GnomAD database, including 30,005 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 0.62 (30005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 5 publications found

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 = 0.814 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: 0.615 AC: 93302 AN: 151776 Hom.: 29949 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.615 AC: 93417 AN: 151896 Hom.: 30005 Cov.: 32 AF XY: 0.612 AC XY: 45401 AN XY: 74224

African (AFR) AF: 0.821 AC: 34038 AN: 41460

American (AMR) AF: 0.636 AC: 9716 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2369 AN: 5154

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4816

European-Finnish (FIN) AF: 0.511 AC: 5364 AN: 10488

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.521 AC: 35421 AN: 67928

Other (OTH) AF: 0.589 AC: 1242 AN: 2110

Alfa AF: 0.565 Hom.: 2929

Bravo AF: 0.632

Asia WGS AF: 0.520 AC: 1811 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	2.3
DANN	Benign	0.51
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs4703647; hg19: chr5-71011512;