14-41504140-T-C

Variant names:

• chr14-41504140-T-C
• rs9285572

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 0.675 in 151,930 control chromosomes in the GnomAD database, including 35,472 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 0.68 (35472 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.675 AC: 102473 AN: 151812 Hom.: 35418 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.675 AC: 102591 AN: 151930 Hom.: 35472 Cov.: 31 AF XY: 0.678 AC XY: 50366 AN XY: 74272

African (AFR) AF: 0.781 AC: 32383 AN: 41458

American (AMR) AF: 0.720 AC: 10960 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5067 AN: 5142

South Asian (SAS) AF: 0.683 AC: 3292 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6334 AN: 10562

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40412 AN: 67944

Other (OTH) AF: 0.635 AC: 1337 AN: 2106

Alfa AF: 0.618 Hom.: 13771

Bravo AF: 0.690

Asia WGS AF: 0.864 AC: 3002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.34
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs9285572; hg19: chr14-41973343;