rs1971791

Variant names:

• chr15-70283799-G-A
• rs1971791
• ENST00000819627.1:n.341-7800G>A

Variant summary

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

The ENST00000819627.1(ENSG00000306606):​n.341-7800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,180 control chromosomes in the GnomAD database, including 16,595 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 0.45 (16595 hom., cov: 33)
• Consequence: ENSG00000306606 ENST00000819627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893
• Publications: 16 publications found

Genes affected

ENSG00000306606 (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 (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819627.1. 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
	ENSG00000306606	ENST00000819627.1		n.341-7800G>A		intron	N/A
	ENSG00000306606	ENST00000819628.1		n.292-7800G>A		intron	N/A
	ENSG00000306606	ENST00000819629.1		n.525-7800G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69126 AN: 152062 Hom.: 16589 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.454 AC: 69141 AN: 152180 Hom.: 16595 Cov.: 33 AF XY: 0.457 AC XY: 33981 AN XY: 74406

African (AFR) AF: 0.295 AC: 12232 AN: 41520

American (AMR) AF: 0.469 AC: 7176 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2429 AN: 5176

South Asian (SAS) AF: 0.465 AC: 2244 AN: 4828

European-Finnish (FIN) AF: 0.564 AC: 5976 AN: 10590

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35910 AN: 67992

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.501 Hom.: 80364

Bravo AF: 0.439

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs1971791; hg19: chr15-70576138;