7-134439253-C-T

Variant names:

• chr7-134439253-C-T
• rs1708414

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 0.777 in 151,872 control chromosomes in the GnomAD database, including 45,939 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 0.78 (45939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.777 AC: 117919 AN: 151754 Hom.: 45896 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.777 AC: 118018 AN: 151872 Hom.: 45939 Cov.: 32 AF XY: 0.781 AC XY: 57988 AN XY: 74238

African (AFR) AF: 0.751 AC: 31091 AN: 41404

American (AMR) AF: 0.817 AC: 12489 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4710 AN: 5168

South Asian (SAS) AF: 0.887 AC: 4260 AN: 4802

European-Finnish (FIN) AF: 0.763 AC: 8054 AN: 10562

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.764 AC: 51865 AN: 67864

Other (OTH) AF: 0.760 AC: 1599 AN: 2104

Alfa AF: 0.770 Hom.: 73022

Bravo AF: 0.782

Asia WGS AF: 0.874 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.78
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1708414; hg19: chr7-134124005;