rs12611071

Variant names:

• chr19-7735475-A-C
• rs12611071
• ENST00000678003.1:n.*291-1501T>G

Variant summary

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

The ENST00000678003.1(ENSG00000288669):​n.*291-1501T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,152 control chromosomes in the GnomAD database, including 42,669 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 0.73 (42669 hom., cov: 33)
• Consequence: ENSG00000288669 ENST00000678003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 4 publications found

Genes affected

ENSG00000288669 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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
ENSG00000288669	ENST00000678003.1	n.*291-1501T>G		intron_variant	Intron 2 of 12			ENSP00000504497.1
ENSG00000288669	ENST00000676543.1	n.71-1501T>G		intron_variant	Intron 1 of 11			ENSP00000503143.1
ENSG00000288669	ENST00000678227.1	n.580-1519T>G		intron_variant	Intron 1 of 1
ENSG00000288669	ENST00000678780.1	n.*1795-1501T>G		intron_variant	Intron 4 of 12			ENSP00000503751.1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110763 AN: 152034 Hom.: 42650 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.728 AC: 110812 AN: 152152 Hom.: 42669 Cov.: 33 AF XY: 0.730 AC XY: 54293 AN XY: 74398

African (AFR) AF: 0.450 AC: 18652 AN: 41456

American (AMR) AF: 0.803 AC: 12281 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2914 AN: 3468

East Asian (EAS) AF: 0.680 AC: 3522 AN: 5176

South Asian (SAS) AF: 0.787 AC: 3793 AN: 4818

European-Finnish (FIN) AF: 0.878 AC: 9312 AN: 10602

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57745 AN: 68026

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.808 Hom.: 187951

Bravo AF: 0.710

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.4
DANN	Benign	0.59
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12611071; hg19: chr19-7800361;