4-132700714-A-T

Variant names:

• chr4-132700714-A-T
• rs10518618

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 0.0854 in 151,412 control chromosomes in the GnomAD database, including 1,168 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 0.085 (1168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.0853 AC: 12903 AN: 151300 Hom.: 1166 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0683

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

GnomAD4 genome AF: 0.0854 AC: 12925 AN: 151412 Hom.: 1168 Cov.: 31 AF XY: 0.0887 AC XY: 6564 AN XY: 74018

African (AFR) AF: 0.197 AC: 8164 AN: 41356

American (AMR) AF: 0.110 AC: 1672 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3464

East Asian (EAS) AF: 0.269 AC: 1387 AN: 5156

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4824

European-Finnish (FIN) AF: 0.0295 AC: 312 AN: 10590

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0129 AC: 872 AN: 67572

Other (OTH) AF: 0.0676 AC: 142 AN: 2100

Alfa AF: 0.0520 Hom.: 62

Bravo AF: 0.0985

Asia WGS AF: 0.154 AC: 530 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10518618; hg19: chr4-133621869; COSMIC: COSV65407958;