chr15-64895021-T-C

Position:

• chr15-64895021-T-C

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 0.72 in 152,068 control chromosomes in the GnomAD database, including 40,633 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 0.72 (40633 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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 (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109397 AN: 151950 Hom.: 40580 Cov.: 31

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.720 AC: 109508 AN: 152068 Hom.: 40633 Cov.: 31 AF XY: 0.723 AC XY: 53691 AN XY: 74302

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.697

Alfa AF: 0.653 Hom.: 14974

Bravo AF: 0.736

Asia WGS AF: 0.888 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1628955; hg19: chr15-65187220;