rs3116651

Variant names:

• chr1-159728695-C-T
• rs3116651
• ENST00000751816.1:n.244+2032C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.244+2032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,048 control chromosomes in the GnomAD database, including 5,318 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 0.24 (5318 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 8 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=-0.88).
• 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.244+2032C>T		intron_variant	Intron 2 of 2
ENSG00000297913	ENST00000751817.1	n.356+1521C>T		intron_variant	Intron 3 of 3
ENSG00000297913	ENST00000751818.1	n.199+2032C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36648 AN: 151930 Hom.: 5317 Cov.: 31

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.241 AC: 36665 AN: 152048 Hom.: 5318 Cov.: 31 AF XY: 0.243 AC XY: 18070 AN XY: 74298

African (AFR) AF: 0.0859 AC: 3562 AN: 41488

American (AMR) AF: 0.301 AC: 4598 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3470

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5180

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4822

European-Finnish (FIN) AF: 0.354 AC: 3736 AN: 10552

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21297 AN: 67928

Other (OTH) AF: 0.254 AC: 538 AN: 2116

Alfa AF: 0.292 Hom.: 8857

Bravo AF: 0.232

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3116651; hg19: chr1-159698485;