4-63661722-T-G

Variant names:

• chr4-63661722-T-G
• rs10517864

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 0.0453 in 151,698 control chromosomes in the GnomAD database, including 190 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 0.045 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0776 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: 0.0452 AC: 6859 AN: 151580 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0457

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0366

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

GnomAD4 genome AF: 0.0453 AC: 6876 AN: 151698 Hom.: 190 Cov.: 32 AF XY: 0.0449 AC XY: 3326 AN XY: 74108

African (AFR) AF: 0.0799 AC: 3317 AN: 41522

American (AMR) AF: 0.0227 AC: 344 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5148

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4828

European-Finnish (FIN) AF: 0.0359 AC: 381 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0335 AC: 2269 AN: 67648

Other (OTH) AF: 0.0362 AC: 76 AN: 2100

Alfa AF: 0.0115 Hom.: 4

Bravo AF: 0.0451

Asia WGS AF: 0.0210 AC: 74 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.67
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs10517864; hg19: chr4-64527440;