rs12980274

Variant names:

• chr19-409977-G-A
• rs12980274
• XM_047439790.1:c.*316C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-409977-G-A
• chr19-409977-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047439790.1(LOC124904607):​c.*316C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,018 control chromosomes in the GnomAD database, including 39,983 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 0.72 (39983 hom., cov: 32)
• Consequence: LOC124904607 XM_047439790.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

Genes affected

LOC124904607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110032 AN: 151900 Hom.: 39929 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.725 AC: 110148 AN: 152018 Hom.: 39983 Cov.: 32 AF XY: 0.726 AC XY: 53916 AN XY: 74304

African (AFR) AF: 0.668 AC: 27675 AN: 41436

American (AMR) AF: 0.759 AC: 11613 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2539 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3681 AN: 5152

South Asian (SAS) AF: 0.767 AC: 3692 AN: 4816

European-Finnish (FIN) AF: 0.744 AC: 7868 AN: 10576

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

European-Non Finnish (NFE) AF: 0.745 AC: 50626 AN: 67970

Other (OTH) AF: 0.733 AC: 1537 AN: 2098

Alfa AF: 0.736 Hom.: 54718

Bravo AF: 0.720

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.88
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12980274; hg19: chr19-409977;