rs1938115

Variant names:

• chr6-65883272-T-C
• rs1938115

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;