rs1936166

chr6-77388936-G-Achr6-77388936-G-Cchr6-77388936-G-T

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 0.907 in 152,030 control chromosomes in the GnomAD database, including 63,354 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 0.91 (63354 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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: 0.908 AC: 137876 AN: 151912 Hom.: 63322 Cov.: 33

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.907 AC: 137960 AN: 152030 Hom.: 63354 Cov.: 33 AF XY: 0.908 AC XY: 67479 AN XY: 74330

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.923

Alfa AF: 0.939 Hom.: 8398

Bravo AF: 0.899

Asia WGS AF: 0.862 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936166; hg19: chr6-78098653;