4-30638650-C-T

Variant names:

• chr4-30638650-C-T
• rs13109270

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 0.335 in 151,884 control chromosomes in the GnomAD database, including 10,656 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 0.34 (10656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.336 AC: 50943 AN: 151766 Hom.: 10649 Cov.: 31

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.335 AC: 50942 AN: 151884 Hom.: 10656 Cov.: 31 AF XY: 0.334 AC XY: 24809 AN XY: 74236

African (AFR) AF: 0.0892 AC: 3696 AN: 41424

American (AMR) AF: 0.386 AC: 5891 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1010 AN: 5150

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4802

European-Finnish (FIN) AF: 0.455 AC: 4794 AN: 10538

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31196 AN: 67942

Other (OTH) AF: 0.383 AC: 807 AN: 2108

Alfa AF: 0.425 Hom.: 17560

Bravo AF: 0.320

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.083
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs13109270; hg19: chr4-30640272;