chr14-41256968-A-G

Variant names:

• chr14-41256968-A-G
• rs1782141

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.745 in 152,114 control chromosomes in the GnomAD database, including 42,453 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 0.75 (42453 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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: 0.745 AC: 113284 AN: 151998 Hom.: 42411 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.745 AC: 113385 AN: 152114 Hom.: 42453 Cov.: 33 AF XY: 0.744 AC XY: 55345 AN XY: 74352

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.770

Alfa AF: 0.751 Hom.: 5334

Bravo AF: 0.755

Asia WGS AF: 0.695 AC: 2416 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1782141; hg19: chr14-41726171;