chr4-113810632-A-G

Variant names:

• chr4-113810632-A-G
• rs12331375

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 0.27 in 151,988 control chromosomes in the GnomAD database, including 6,631 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 (6631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.270 AC: 41028 AN: 151874 Hom.: 6634 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.270 AC: 41031 AN: 151988 Hom.: 6631 Cov.: 32 AF XY: 0.274 AC XY: 20380 AN XY: 74282

African (AFR) AF: 0.0959 AC: 3981 AN: 41516

American (AMR) AF: 0.310 AC: 4723 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2464 AN: 5168

South Asian (SAS) AF: 0.485 AC: 2335 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3352 AN: 10540

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22147 AN: 67908

Other (OTH) AF: 0.289 AC: 608 AN: 2106

Alfa AF: 0.278 Hom.: 1049

Bravo AF: 0.258

Asia WGS AF: 0.456 AC: 1586 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12331375; hg19: chr4-114731788;