rs6538761

Variant names:

• chr12-97040442-A-C
• rs6538761
• ENST00000549896.1:n.190+7019A>C

Variant summary

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

The ENST00000549896.1(ENSG00000257470):​n.190+7019A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,056 control chromosomes in the GnomAD database, including 33,255 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 0.66 (33255 hom., cov: 32)
• Consequence: ENSG00000257470 ENST00000549896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 9 publications found

Genes affected

ENSG00000257470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 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
ENSG00000257470	ENST00000549896.1	n.190+7019A>C		intron_variant	Intron 2 of 2	5
ENSG00000257470	ENST00000666269.1	n.255+7019A>C		intron_variant	Intron 3 of 3
ENSG00000257470	ENST00000668647.1	n.297+7019A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100303 AN: 151938 Hom.: 33212 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.660 AC: 100405 AN: 152056 Hom.: 33255 Cov.: 32 AF XY: 0.659 AC XY: 48971 AN XY: 74338

African (AFR) AF: 0.705 AC: 29253 AN: 41470

American (AMR) AF: 0.657 AC: 10033 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2469 AN: 5152

South Asian (SAS) AF: 0.553 AC: 2668 AN: 4824

European-Finnish (FIN) AF: 0.680 AC: 7189 AN: 10576

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44571 AN: 67980

Other (OTH) AF: 0.653 AC: 1375 AN: 2106

Alfa AF: 0.652 Hom.: 132908

Bravo AF: 0.661

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.78
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6538761; hg19: chr12-97434220;