4-46150315-T-C

Variant names:

• chr4-46150315-T-C
• rs10033451

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 0.429 in 152,008 control chromosomes in the GnomAD database, including 14,504 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 0.43 (14504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65225 AN: 151890 Hom.: 14491 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.429 AC: 65281 AN: 152008 Hom.: 14504 Cov.: 32 AF XY: 0.425 AC XY: 31592 AN XY: 74300

African (AFR) AF: 0.365 AC: 15125 AN: 41462

American (AMR) AF: 0.411 AC: 6276 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1573 AN: 5156

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4828

European-Finnish (FIN) AF: 0.462 AC: 4874 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33282 AN: 67944

Other (OTH) AF: 0.421 AC: 889 AN: 2114

Alfa AF: 0.462 Hom.: 61044

Bravo AF: 0.424

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10033451; hg19: chr4-46152332;