4-31360317-T-C

Variant names:

• chr4-31360317-T-C
• rs10033498

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 0.438 in 152,056 control chromosomes in the GnomAD database, including 15,311 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 0.44 (15311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.438 AC: 66527 AN: 151938 Hom.: 15305 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.438 AC: 66558 AN: 152056 Hom.: 15311 Cov.: 33 AF XY: 0.446 AC XY: 33113 AN XY: 74312

African (AFR) AF: 0.384 AC: 15911 AN: 41476

American (AMR) AF: 0.485 AC: 7413 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4396 AN: 5168

South Asian (SAS) AF: 0.609 AC: 2939 AN: 4824

European-Finnish (FIN) AF: 0.445 AC: 4699 AN: 10558

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28152 AN: 67962

Other (OTH) AF: 0.452 AC: 954 AN: 2112

Alfa AF: 0.420 Hom.: 2966

Bravo AF: 0.437

Asia WGS AF: 0.708 AC: 2458 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.41
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10033498; hg19: chr4-31361939;