rs13222675

Positions:

• chr7-86282105-T-C

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 0.0682 in 152,236 control chromosomes in the GnomAD database, including 503 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 0.068 (503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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: 0.0683 AC: 10388 AN: 152118 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0682 AC: 10387 AN: 152236 Hom.: 503 Cov.: 32 AF XY: 0.0676 AC XY: 5035 AN XY: 74448

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0359

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0898 Hom.: 331

Bravo AF: 0.0592

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13222675; hg19: chr7-85911421;