rs6973441

Variant names:

• chr7-153534402-G-T
• rs6973441

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.443

Alfa AF: 0.448 Hom.: 3721

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6973441; hg19: chr7-153231487;