rs4308625

Variant names:

• chr7-14003077-T-C
• rs4308625

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 0.272 in 151,182 control chromosomes in the GnomAD database, including 6,673 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 0.27 (6673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 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: 0.272 AC: 41079 AN: 151058 Hom.: 6644 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.272 AC: 41166 AN: 151182 Hom.: 6673 Cov.: 31 AF XY: 0.275 AC XY: 20306 AN XY: 73830

African (AFR) AF: 0.461 AC: 18979 AN: 41194

American (AMR) AF: 0.255 AC: 3881 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1117 AN: 5034

South Asian (SAS) AF: 0.135 AC: 647 AN: 4784

European-Finnish (FIN) AF: 0.244 AC: 2546 AN: 10428

Middle Eastern (MID) AF: 0.318 AC: 91 AN: 286

European-Non Finnish (NFE) AF: 0.179 AC: 12115 AN: 67766

Other (OTH) AF: 0.245 AC: 516 AN: 2110

Alfa AF: 0.216 Hom.: 956

Bravo AF: 0.285

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.12
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4308625; hg19: chr7-14042702;