rs6957003

chr7-113232951-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0258 in 152,246 control chromosomes in the GnomAD database, including 79 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 0.026 (79 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0258 (3931/152246) while in subpopulation AFR AF= 0.0444 (1846/41552). AF 95% confidence interval is 0.0427. There are 79 homozygotes in gnomad4. There are 1924 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 79 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0258 AC: 3930 AN: 152128 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0258 AC: 3931 AN: 152246 Hom.: 79 Cov.: 32 AF XY: 0.0258 AC XY: 1924 AN XY: 74438

Gnomad4 AFR AF: 0.0444

Gnomad4 AMR AF: 0.0154

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0231 Hom.: 8

Bravo AF: 0.0262

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.68
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6957003; hg19: chr7-112873006;