chr6-153945539-A-T

Variant names:

• chr6-153945539-A-T
• rs7741685

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 0.345 in 152,024 control chromosomes in the GnomAD database, including 9,182 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 0.35 (9182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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: 0.345 AC: 52410 AN: 151906 Hom.: 9163 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.345 AC: 52467 AN: 152024 Hom.: 9182 Cov.: 32 AF XY: 0.352 AC XY: 26198 AN XY: 74340

African (AFR) AF: 0.313 AC: 12972 AN: 41452

American (AMR) AF: 0.466 AC: 7122 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2573 AN: 5148

South Asian (SAS) AF: 0.478 AC: 2306 AN: 4824

European-Finnish (FIN) AF: 0.316 AC: 3345 AN: 10570

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21458 AN: 67964

Other (OTH) AF: 0.374 AC: 788 AN: 2108

Alfa AF: 0.337 Hom.: 1079

Bravo AF: 0.349

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.38
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7741685; hg19: chr6-154266674;