rs1782182

Positions:

• chr14-41227938-G-A
• chr14-41227938-G-C

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 0.754 in 151,484 control chromosomes in the GnomAD database, including 43,283 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 (43283 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114129 AN: 151370 Hom.: 43226 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.754 AC: 114248 AN: 151484 Hom.: 43283 Cov.: 30 AF XY: 0.753 AC XY: 55736 AN XY: 74008

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.776

Alfa AF: 0.749 Hom.: 4048

Bravo AF: 0.764

Asia WGS AF: 0.706 AC: 2449 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1782182; hg19: chr14-41697141;