rs6973441

Variant names:

• chr7-153534402-G-T
• rs6973441

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 0.401 in 151,836 control chromosomes in the GnomAD database, including 13,468 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 0.40 (13468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 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: 0.402 AC: 60920 AN: 151720 Hom.: 13471 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.401 AC: 60932 AN: 151836 Hom.: 13468 Cov.: 31 AF XY: 0.394 AC XY: 29252 AN XY: 74182

African (AFR) AF: 0.266 AC: 11010 AN: 41378

American (AMR) AF: 0.442 AC: 6738 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3468

East Asian (EAS) AF: 0.0980 AC: 504 AN: 5144

South Asian (SAS) AF: 0.440 AC: 2113 AN: 4802

European-Finnish (FIN) AF: 0.351 AC: 3695 AN: 10540

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33465 AN: 67942

Other (OTH) AF: 0.443 AC: 934 AN: 2108

Alfa AF: 0.450 Hom.: 5942

Bravo AF: 0.399

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6973441; hg19: chr7-153231487;