chr6-160776526-T-C

Variant names:

• chr6-160776526-T-C
• rs1740442

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 0.589 in 152,110 control chromosomes in the GnomAD database, including 26,991 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 0.59 (26991 hom., cov: 33)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 6 publications found

Genes affected

LOC107986665 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619095.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274903	ENST00000619095.1	TSL:6	n.45+2494T>C		intron	N/A
	ENSG00000303572	ENST00000795697.1		n.244-85A>G		intron	N/A
	ENSG00000303572	ENST00000795698.1		n.218-85A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89502 AN: 151992 Hom.: 26960 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.589 AC: 89579 AN: 152110 Hom.: 26991 Cov.: 33 AF XY: 0.596 AC XY: 44344 AN XY: 74348

African (AFR) AF: 0.596 AC: 24741 AN: 41490

American (AMR) AF: 0.685 AC: 10471 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1757 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5086 AN: 5180

South Asian (SAS) AF: 0.715 AC: 3450 AN: 4826

European-Finnish (FIN) AF: 0.534 AC: 5642 AN: 10568

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36417 AN: 67976

Other (OTH) AF: 0.622 AC: 1315 AN: 2114

Alfa AF: 0.566 Hom.: 39103

Bravo AF: 0.600

Asia WGS AF: 0.832 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1740442; hg19: chr6-161197558;