chr1-159696131-C-G

Variant names:

• chr1-159696131-C-G
• rs2808624
• ENST00000751816.1:n.108-30396C>G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-30396C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,848 control chromosomes in the GnomAD database, including 9,839 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 0.35 (9839 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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.108-30396C>G		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-30396C>G		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-30396C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52639 AN: 151730 Hom.: 9835 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.347 AC: 52660 AN: 151848 Hom.: 9839 Cov.: 32 AF XY: 0.349 AC XY: 25912 AN XY: 74206

African (AFR) AF: 0.210 AC: 8677 AN: 41406

American (AMR) AF: 0.406 AC: 6195 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3468

East Asian (EAS) AF: 0.581 AC: 3000 AN: 5164

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4818

European-Finnish (FIN) AF: 0.390 AC: 4106 AN: 10524

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26417 AN: 67920

Other (OTH) AF: 0.364 AC: 768 AN: 2108

Alfa AF: 0.229 Hom.: 561

Bravo AF: 0.341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.27
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2808624; hg19: chr1-159665921;