15-77872364-T-C

Position:

• chr15-77872364-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 0.49 in 151,908 control chromosomes in the GnomAD database, including 19,439 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 0.49 (19439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74267 AN: 151790 Hom.: 19401 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.490 AC: 74363 AN: 151908 Hom.: 19439 Cov.: 32 AF XY: 0.486 AC XY: 36105 AN XY: 74240

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.441

Alfa AF: 0.404 Hom.: 11918

Bravo AF: 0.505

Asia WGS AF: 0.389 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11857176; hg19: chr15-78164706;