rs683493

Variant names:

• chr7-126165247-G-A
• rs683493

Your query was ambiguous. Multiple possible variants found:

• chr7-126165247-G-A
• chr7-126165247-G-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 0.352 in 151,418 control chromosomes in the GnomAD database, including 13,333 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 0.35 (13333 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.351 AC: 53146 AN: 151300 Hom.: 13286 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.352 AC: 53236 AN: 151418 Hom.: 13333 Cov.: 31 AF XY: 0.352 AC XY: 26066 AN XY: 73996

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.282

Alfa AF: 0.201 Hom.: 4708

Bravo AF: 0.361

Asia WGS AF: 0.272 AC: 943 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs683493; hg19: chr7-125805301;