chr1-159725971-A-G

Variant names:

• chr1-159725971-A-G
• rs3116654
• ENST00000751816.1:n.108-556A>G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,198 control chromosomes in the GnomAD database, including 847 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 0.093 (847 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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.108-556A>G		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-556A>G		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-556A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14174 AN: 152080 Hom.: 845 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.0932 AC: 14178 AN: 152198 Hom.: 847 Cov.: 32 AF XY: 0.0941 AC XY: 7001 AN XY: 74388

African (AFR) AF: 0.0224 AC: 929 AN: 41552

American (AMR) AF: 0.0934 AC: 1426 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5184

South Asian (SAS) AF: 0.102 AC: 492 AN: 4824

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8781 AN: 67986

Other (OTH) AF: 0.0996 AC: 210 AN: 2108

Alfa AF: 0.111 Hom.: 1702

Bravo AF: 0.0853

Asia WGS AF: 0.0600 AC: 209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3116654; hg19: chr1-159695761;