4-63092452-T-C

Variant names:

• chr4-63092452-T-C
• rs4349629

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 0.597 in 151,996 control chromosomes in the GnomAD database, including 28,391 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 0.60 (28391 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 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: 0.597 AC: 90735 AN: 151878 Hom.: 28389 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.597 AC: 90773 AN: 151996 Hom.: 28391 Cov.: 33 AF XY: 0.592 AC XY: 43958 AN XY: 74308

African (AFR) AF: 0.419 AC: 17353 AN: 41434

American (AMR) AF: 0.665 AC: 10142 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2273 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1856 AN: 5144

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7037 AN: 10576

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47407 AN: 67976

Other (OTH) AF: 0.629 AC: 1330 AN: 2116

Alfa AF: 0.640 Hom.: 10380

Bravo AF: 0.595

Asia WGS AF: 0.431 AC: 1502 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	1.9
DANN	Benign	0.83
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4349629; hg19: chr4-63958170;