chr4-106513562-G-T

Variant names:

• chr4-106513562-G-T
• rs2903418

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 0.406 in 151,906 control chromosomes in the GnomAD database, including 12,645 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 0.41 (12645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.406 AC: 61607 AN: 151788 Hom.: 12628 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.406 AC: 61659 AN: 151906 Hom.: 12645 Cov.: 32 AF XY: 0.403 AC XY: 29920 AN XY: 74242

African (AFR) AF: 0.438 AC: 18132 AN: 41420

American (AMR) AF: 0.461 AC: 7031 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3464

East Asian (EAS) AF: 0.396 AC: 2044 AN: 5156

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4828

European-Finnish (FIN) AF: 0.337 AC: 3555 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26396 AN: 67912

Other (OTH) AF: 0.391 AC: 823 AN: 2104

Alfa AF: 0.379 Hom.: 9249

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2903418; hg19: chr4-107434719;