10-43678196-G-A

Variant names:

• chr10-43678196-G-A
• rs2484665

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 0.388 in 151,732 control chromosomes in the GnomAD database, including 11,589 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 0.39 (11589 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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: 0.387 AC: 58726 AN: 151614 Hom.: 11565 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.388 AC: 58797 AN: 151732 Hom.: 11589 Cov.: 31 AF XY: 0.385 AC XY: 28519 AN XY: 74152

African (AFR) AF: 0.442 AC: 18278 AN: 41330

American (AMR) AF: 0.399 AC: 6077 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1469 AN: 5152

South Asian (SAS) AF: 0.388 AC: 1860 AN: 4792

European-Finnish (FIN) AF: 0.345 AC: 3631 AN: 10528

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25269 AN: 67926

Other (OTH) AF: 0.382 AC: 806 AN: 2108

Alfa AF: 0.287 Hom.: 984

Bravo AF: 0.394

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.57
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2484665; hg19: chr10-44173644;