rs12410279

Variant names:

• chr1-220678178-A-G
• rs12410279

Your query was ambiguous. Multiple possible variants found:

• chr1-220678178-A-G
• chr1-220678178-A-T

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 0.129 in 151,940 control chromosomes in the GnomAD database, including 1,863 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 0.13 (1863 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 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: 0.129 AC: 19583 AN: 151822 Hom.: 1859 Cov.: 31

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.129 AC: 19587 AN: 151940 Hom.: 1863 Cov.: 31 AF XY: 0.135 AC XY: 10016 AN XY: 74242

African (AFR) AF: 0.0320 AC: 1329 AN: 41488

American (AMR) AF: 0.226 AC: 3452 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1907 AN: 5134

South Asian (SAS) AF: 0.210 AC: 1010 AN: 4808

European-Finnish (FIN) AF: 0.167 AC: 1764 AN: 10544

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9171 AN: 67938

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.143 Hom.: 4357

Bravo AF: 0.137

Asia WGS AF: 0.237 AC: 813 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12410279; hg19: chr1-220851520;