rs12103880

Variant names:

• chr17-9795025-G-A
• rs12103880
• ENST00000609065.1:n.139-3735C>T

Variant summary

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

The ENST00000609065.1(ENSG00000278944):​n.139-3735C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,114 control chromosomes in the GnomAD database, including 5,774 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 0.25 (5774 hom., cov: 32)
• Consequence: ENSG00000278944 ENST00000609065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 9 publications found

Genes affected

ENSG00000278944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609065.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000278944	ENST00000609065.1	TSL:5	n.139-3735C>T		intron	N/A
	ENSG00000282882	ENST00000634974.2	TSL:5	n.283-8758G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38093 AN: 151998 Hom.: 5771 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.251 AC: 38140 AN: 152114 Hom.: 5774 Cov.: 32 AF XY: 0.241 AC XY: 17930 AN XY: 74338

African (AFR) AF: 0.429 AC: 17794 AN: 41490

American (AMR) AF: 0.138 AC: 2118 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3468

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5178

South Asian (SAS) AF: 0.0913 AC: 440 AN: 4820

European-Finnish (FIN) AF: 0.175 AC: 1851 AN: 10576

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14361 AN: 67970

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.219 Hom.: 17873

Bravo AF: 0.257

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12103880;

hg19: chr17-9698342;

COSMIC: COSV57652492;