14-32318941-T-C

Variant names:

• chr14-32318941-T-C
• rs11623278

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 0.535 in 151,986 control chromosomes in the GnomAD database, including 22,509 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 0.54 (22509 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.535 AC: 81239 AN: 151868 Hom.: 22460 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.535 AC: 81350 AN: 151986 Hom.: 22509 Cov.: 31 AF XY: 0.535 AC XY: 39760 AN XY: 74288

African (AFR) AF: 0.691 AC: 28630 AN: 41458

American (AMR) AF: 0.549 AC: 8383 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2514 AN: 5160

South Asian (SAS) AF: 0.557 AC: 2680 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4563 AN: 10562

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31368 AN: 67948

Other (OTH) AF: 0.509 AC: 1070 AN: 2102

Alfa AF: 0.520 Hom.: 4069

Bravo AF: 0.547

Asia WGS AF: 0.583 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.45
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs11623278; hg19: chr14-32788147;