chr4-63661722-T-G

Position:

• chr4-63661722-T-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.63661722T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0799

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0362

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517864; hg19: chr4-64527440;