rs12249418

Variant names:

• chr10-94683160-T-A
• rs12249418

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 0.2 in 152,104 control chromosomes in the GnomAD database, including 3,227 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 0.20 (3227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.200 AC: 30383 AN: 151986 Hom.: 3226 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30385 AN: 152104 Hom.: 3227 Cov.: 32 AF XY: 0.196 AC XY: 14594 AN XY: 74358

African (AFR) AF: 0.221 AC: 9175 AN: 41484

American (AMR) AF: 0.133 AC: 2026 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3470

East Asian (EAS) AF: 0.00947 AC: 49 AN: 5172

South Asian (SAS) AF: 0.164 AC: 789 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1935 AN: 10586

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14945 AN: 67988

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.221 Hom.: 496

Bravo AF: 0.196

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.26
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs12249418; hg19: chr10-96442917;