6-160768638-A-G

Variant names:

• chr6-160768638-A-G
• rs1247557

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.440 AC: 18229 AN: 41446

American (AMR) AF: 0.653 AC: 9972 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.980 AC: 5075 AN: 5176

South Asian (SAS) AF: 0.681 AC: 3284 AN: 4820

European-Finnish (FIN) AF: 0.530 AC: 5607 AN: 10576

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35967 AN: 67976

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.552 Hom.: 4115

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1247557; hg19: chr6-161189670;