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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.718 AC: 29669 AN: 41346

American (AMR) AF: 0.241 AC: 3651 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3454

East Asian (EAS) AF: 0.313 AC: 1607 AN: 5132

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4812

European-Finnish (FIN) AF: 0.326 AC: 3433 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12478 AN: 67642

Other (OTH) AF: 0.282 AC: 593 AN: 2104

Alfa AF: 0.235 Hom.: 11292

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
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs683493; hg19: chr7-125805301;