rs4444235

Variant names:

• chr14-53944201-T-C
• rs4444235

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 0.43 in 152,106 control chromosomes in the GnomAD database, including 14,506 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 (14506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 180 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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: 0.431 AC: 65438 AN: 151988 Hom.: 14503 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.430 AC: 65474 AN: 152106 Hom.: 14506 Cov.: 32 AF XY: 0.432 AC XY: 32152 AN XY: 74352

African (AFR) AF: 0.332 AC: 13770 AN: 41496

American (AMR) AF: 0.480 AC: 7338 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2449 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4411 AN: 10572

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31423 AN: 67970

Other (OTH) AF: 0.481 AC: 1017 AN: 2114

Alfa AF: 0.464 Hom.: 78682

Bravo AF: 0.430

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.55
DANN	Benign	0.82
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs4444235; hg19: chr14-54410919;