4-30666913-G-T

Variant names:

• chr4-30666913-G-T
• rs13146789

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 0.323 in 152,010 control chromosomes in the GnomAD database, including 9,772 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 0.32 (9772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.433 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: 0.323 AC: 49030 AN: 151892 Hom.: 9766 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.323 AC: 49033 AN: 152010 Hom.: 9772 Cov.: 32 AF XY: 0.322 AC XY: 23927 AN XY: 74272

African (AFR) AF: 0.0877 AC: 3639 AN: 41514

American (AMR) AF: 0.387 AC: 5907 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5164

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4574 AN: 10532

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

European-Non Finnish (NFE) AF: 0.437 AC: 29677 AN: 67950

Other (OTH) AF: 0.355 AC: 749 AN: 2110

Alfa AF: 0.396 Hom.: 39137

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.37
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs13146789; hg19: chr4-30668535;