chr7-14113185-A-G

Variant names:

• chr7-14113185-A-G
• rs2357842

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 0.946 in 152,196 control chromosomes in the GnomAD database, including 68,173 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 0.95 (68173 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.946 AC: 143818 AN: 152078 Hom.: 68113 Cov.: 31

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.946 AC: 143938 AN: 152196 Hom.: 68173 Cov.: 31 AF XY: 0.949 AC XY: 70582 AN XY: 74380

African (AFR) AF: 0.984 AC: 40879 AN: 41564

American (AMR) AF: 0.976 AC: 14908 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3413 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5134 AN: 5136

South Asian (SAS) AF: 0.980 AC: 4711 AN: 4808

European-Finnish (FIN) AF: 0.926 AC: 9811 AN: 10590

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61912 AN: 68028

Other (OTH) AF: 0.966 AC: 2043 AN: 2114

Alfa AF: 0.930 Hom.: 134580

Bravo AF: 0.952

Asia WGS AF: 0.990 AC: 3443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.82
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2357842; hg19: chr7-14152810;