6-153945430-T-G

Variant names:

• chr6-153945430-T-G
• rs7745695

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 0.378 in 152,032 control chromosomes in the GnomAD database, including 11,060 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 0.38 (11060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.377 AC: 57344 AN: 151914 Hom.: 11033 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.378 AC: 57410 AN: 152032 Hom.: 11060 Cov.: 32 AF XY: 0.384 AC XY: 28537 AN XY: 74320

African (AFR) AF: 0.426 AC: 17669 AN: 41430

American (AMR) AF: 0.476 AC: 7270 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2580 AN: 5168

South Asian (SAS) AF: 0.485 AC: 2331 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3355 AN: 10576

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21473 AN: 67988

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.336 Hom.: 10083

Bravo AF: 0.386

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7745695; hg19: chr6-154266565;