rs7694802

Variant names:

• chr4-103481090-T-C
• rs7694802

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 0.396 in 149,322 control chromosomes in the GnomAD database, including 14,042 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 0.40 (14042 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.395 AC: 59025 AN: 149244 Hom.: 14019 Cov.: 27

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.396 AC: 59069 AN: 149322 Hom.: 14042 Cov.: 27 AF XY: 0.385 AC XY: 28050 AN XY: 72872

African (AFR) AF: 0.665 AC: 27099 AN: 40746

American (AMR) AF: 0.330 AC: 4954 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1098 AN: 3456

East Asian (EAS) AF: 0.0825 AC: 422 AN: 5116

South Asian (SAS) AF: 0.280 AC: 1328 AN: 4746

European-Finnish (FIN) AF: 0.214 AC: 2043 AN: 9526

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.310 AC: 20889 AN: 67460

Other (OTH) AF: 0.383 AC: 790 AN: 2064

Alfa AF: 0.342 Hom.: 13021

Bravo AF: 0.414

Asia WGS AF: 0.214 AC: 745 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.047
DANN	Benign	0.45
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs7694802; hg19: chr4-104402247;