rs1938115

Positions:

• chr6-65883272-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 0.555 in 152,024 control chromosomes in the GnomAD database, including 23,655 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 0.55 (23655 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.555 AC: 84258 AN: 151906 Hom.: 23623 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.555 AC: 84347 AN: 152024 Hom.: 23655 Cov.: 33 AF XY: 0.565 AC XY: 41996 AN XY: 74306

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.564

Alfa AF: 0.547 Hom.: 2897

Bravo AF: 0.556

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938115; hg19: chr6-66593165;