5-71717820-T-C

Variant names:

• chr5-71717820-T-C
• rs3763153

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 0.303 in 151,892 control chromosomes in the GnomAD database, including 6,948 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 0.30 (6948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45999 AN: 151774 Hom.: 6941 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.303 AC: 46043 AN: 151892 Hom.: 6948 Cov.: 32 AF XY: 0.304 AC XY: 22561 AN XY: 74240

African (AFR) AF: 0.271 AC: 11213 AN: 41436

American (AMR) AF: 0.308 AC: 4696 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1586 AN: 5176

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4810

European-Finnish (FIN) AF: 0.342 AC: 3604 AN: 10524

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21327 AN: 67918

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.311 Hom.: 20143

Bravo AF: 0.300

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs3763153; hg19: chr5-71013647;