rs12978960

Variant names:

• chr19-35213334-A-G
• rs12978960
• ENST00000723934.1:n.177-2301A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-35213334-A-G
• chr19-35213334-A-T

Variant summary

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

The ENST00000723934.1(ENSG00000294495):​n.177-2301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,054 control chromosomes in the GnomAD database, including 62,206 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 0.90 (62206 hom., cov: 29)
• Consequence: ENSG00000294495 ENST00000723934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 5 publications found

Genes affected

ENSG00000294495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723934.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000294495	ENST00000723934.1		n.177-2301A>G		intron	N/A
	ENSG00000294495	ENST00000723935.1		n.-129A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137239 AN: 151936 Hom.: 62148 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.903 AC: 137358 AN: 152054 Hom.: 62206 Cov.: 29 AF XY: 0.904 AC XY: 67141 AN XY: 74312

African (AFR) AF: 0.957 AC: 39713 AN: 41504

American (AMR) AF: 0.883 AC: 13466 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3000 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3723 AN: 5142

South Asian (SAS) AF: 0.884 AC: 4247 AN: 4804

European-Finnish (FIN) AF: 0.902 AC: 9528 AN: 10562

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60679 AN: 68002

Other (OTH) AF: 0.915 AC: 1931 AN: 2110

Alfa AF: 0.901 Hom.: 7685

Bravo AF: 0.904

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.92
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs12978960; hg19: chr19-35704237;