chr6-160293044-T-G

Variant names:

• chr6-160293044-T-G
• rs2504954

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 0.275 in 152,030 control chromosomes in the GnomAD database, including 5,836 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 0.28 (5836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.275 AC: 41760 AN: 151912 Hom.: 5818 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.275 AC: 41815 AN: 152030 Hom.: 5836 Cov.: 33 AF XY: 0.278 AC XY: 20663 AN XY: 74308

African (AFR) AF: 0.315 AC: 13060 AN: 41472

American (AMR) AF: 0.260 AC: 3972 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.181 AC: 939 AN: 5174

South Asian (SAS) AF: 0.287 AC: 1383 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3036 AN: 10530

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17715 AN: 67970

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.270 Hom.: 934

Bravo AF: 0.277

Asia WGS AF: 0.254 AC: 879 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.70
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2504954; hg19: chr6-160714076;