rs6973441

Positions:

• chr7-153534402-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;