rs1782144

Variant names:

• chr14-41260570-G-A
• rs1782144

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 0.747 in 152,072 control chromosomes in the GnomAD database, including 42,611 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 (42611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.747 AC: 113499 AN: 151954 Hom.: 42568 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.747 AC: 113602 AN: 152072 Hom.: 42611 Cov.: 32 AF XY: 0.746 AC XY: 55427 AN XY: 74318

African (AFR) AF: 0.789 AC: 32745 AN: 41486

American (AMR) AF: 0.782 AC: 11945 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3675 AN: 5170

South Asian (SAS) AF: 0.653 AC: 3146 AN: 4818

European-Finnish (FIN) AF: 0.682 AC: 7201 AN: 10564

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.731 AC: 49664 AN: 67980

Other (OTH) AF: 0.770 AC: 1627 AN: 2112

Alfa AF: 0.753 Hom.: 5594

Bravo AF: 0.756

Asia WGS AF: 0.694 AC: 2415 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.69
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs1782144; hg19: chr14-41729773;