rs320688

Variant names:

• chr7-137357478-A-C
• rs320688

Your query was ambiguous. Multiple possible variants found:

• chr7-137357478-A-C
• chr7-137357478-A-T

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 0.672 in 151,990 control chromosomes in the GnomAD database, including 34,414 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 0.67 (34414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.672 AC: 102028 AN: 151872 Hom.: 34368 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.672 AC: 102125 AN: 151990 Hom.: 34414 Cov.: 32 AF XY: 0.669 AC XY: 49687 AN XY: 74296

African (AFR) AF: 0.739 AC: 30630 AN: 41456

American (AMR) AF: 0.638 AC: 9737 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3503 AN: 5162

South Asian (SAS) AF: 0.674 AC: 3253 AN: 4828

European-Finnish (FIN) AF: 0.651 AC: 6866 AN: 10552

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43987 AN: 67938

Other (OTH) AF: 0.677 AC: 1428 AN: 2108

Alfa AF: 0.566 Hom.: 1716

Bravo AF: 0.669

Asia WGS AF: 0.664 AC: 2304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs320688; hg19: chr7-137042224;