rs12037277

Variant names:

• chr1-79805653-T-A
• rs12037277

Your query was ambiguous. Multiple possible variants found:

• chr1-79805653-T-A
• chr1-79805653-T-C

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 0.645 in 152,028 control chromosomes in the GnomAD database, including 31,975 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 0.65 (31975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98057 AN: 151908 Hom.: 31955 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.645 AC: 98129 AN: 152028 Hom.: 31975 Cov.: 32 AF XY: 0.650 AC XY: 48321 AN XY: 74322

African (AFR) AF: 0.568 AC: 23537 AN: 41442

American (AMR) AF: 0.742 AC: 11354 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2691 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3820 AN: 5160

South Asian (SAS) AF: 0.673 AC: 3242 AN: 4814

European-Finnish (FIN) AF: 0.686 AC: 7252 AN: 10574

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43956 AN: 67952

Other (OTH) AF: 0.665 AC: 1405 AN: 2114

Alfa AF: 0.642 Hom.: 3958

Bravo AF: 0.648

Asia WGS AF: 0.668 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.60
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12037277; hg19: chr1-80271338;