rs10847980

Variant names:

• chr12-122903375-T-G
• rs10847980
• ENST00000780554.1:n.106-222T>G

Variant summary

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

The ENST00000780554.1(ENSG00000301649):​n.106-222T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,166 control chromosomes in the GnomAD database, including 1,937 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 (1937 hom., cov: 31)
• Consequence: ENSG00000301649 ENST00000780554.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 15 publications found

Genes affected

ENSG00000301649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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
ENSG00000301649	ENST00000780554.1	n.106-222T>G		intron_variant	Intron 1 of 1
ENSG00000301649	ENST00000780555.1	n.106-222T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19605 AN: 152048 Hom.: 1924 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.129 AC: 19660 AN: 152166 Hom.: 1937 Cov.: 31 AF XY: 0.127 AC XY: 9457 AN XY: 74404

African (AFR) AF: 0.273 AC: 11325 AN: 41468

American (AMR) AF: 0.107 AC: 1635 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.193 AC: 998 AN: 5184

South Asian (SAS) AF: 0.127 AC: 614 AN: 4820

European-Finnish (FIN) AF: 0.0337 AC: 358 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0608 AC: 4133 AN: 68016

Other (OTH) AF: 0.131 AC: 276 AN: 2114

Alfa AF: 0.0862 Hom.: 1551

Bravo AF: 0.143

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10847980; hg19: chr12-123387922;