rs1247557

chr6-160768638-A-Gchr6-160768638-A-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 0.538 in 152,058 control chromosomes in the GnomAD database, including 22,895 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 0.54 (22895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.537 AC: 81659 AN: 151940 Hom.: 22868 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.538 AC: 81734 AN: 152058 Hom.: 22895 Cov.: 32 AF XY: 0.545 AC XY: 40482 AN XY: 74320

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.565

Alfa AF: 0.556 Hom.: 4037

Bravo AF: 0.543

Asia WGS AF: 0.808 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.0
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1247557; hg19: chr6-161189670;