rs7690467

Variant names:

• chr4-132405240-T-C
• rs7690467

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 0.34 in 151,820 control chromosomes in the GnomAD database, including 9,216 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 0.34 (9216 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 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: 0.340 AC: 51537 AN: 151702 Hom.: 9173 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.340 AC: 51645 AN: 151820 Hom.: 9216 Cov.: 31 AF XY: 0.343 AC XY: 25466 AN XY: 74182

African (AFR) AF: 0.386 AC: 15994 AN: 41394

American (AMR) AF: 0.456 AC: 6951 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2271 AN: 5142

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4814

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10536

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19327 AN: 67908

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.327 Hom.: 7025

Bravo AF: 0.357

Asia WGS AF: 0.386 AC: 1332 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.34
DANN	Benign	0.76
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs7690467; hg19: chr4-133326395;