rs3116636

Variant names:

• chr1-159716693-G-A
• rs3116636
• ENST00000751816.1:n.108-9834G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-9834G>A 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 150,436 control chromosomes in the GnomAD database, including 5,408 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 (5408 hom., cov: 30)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 3 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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
ENSG00000297913	ENST00000751816.1	n.108-9834G>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-9834G>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-9834G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 37751 AN: 150364 Hom.: 5407 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.251 AC: 37775 AN: 150436 Hom.: 5408 Cov.: 30 AF XY: 0.253 AC XY: 18525 AN XY: 73318

African (AFR) AF: 0.121 AC: 4977 AN: 41016

American (AMR) AF: 0.302 AC: 4579 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1060 AN: 3468

East Asian (EAS) AF: 0.0602 AC: 308 AN: 5114

South Asian (SAS) AF: 0.244 AC: 1166 AN: 4786

European-Finnish (FIN) AF: 0.355 AC: 3518 AN: 9918

Middle Eastern (MID) AF: 0.223 AC: 63 AN: 282

European-Non Finnish (NFE) AF: 0.314 AC: 21238 AN: 67730

Other (OTH) AF: 0.261 AC: 541 AN: 2072

Alfa AF: 0.298 Hom.: 8701

Bravo AF: 0.244

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.27
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs3116636; hg19: chr1-159686483;