rs1703975

Variant names:

• chr8-8719829-C-G
• rs1703975
• ENST00000765578.1:n.660+3701G>C

Variant summary

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

The ENST00000765578.1(ENSG00000254367):​n.660+3701G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,184 control chromosomes in the GnomAD database, including 2,065 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 0.15 (2065 hom., cov: 33)
• Consequence: ENSG00000254367 ENST00000765578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 2 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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
ENSG00000254367	ENST00000765578.1	n.660+3701G>C		intron_variant	Intron 3 of 3
ENSG00000254367	ENST00000765579.1	n.741-299G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23073 AN: 152066 Hom.: 2067 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.152 AC: 23088 AN: 152184 Hom.: 2065 Cov.: 33 AF XY: 0.151 AC XY: 11221 AN XY: 74408

African (AFR) AF: 0.254 AC: 10517 AN: 41474

American (AMR) AF: 0.118 AC: 1800 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.110 AC: 570 AN: 5186

South Asian (SAS) AF: 0.0751 AC: 363 AN: 4832

European-Finnish (FIN) AF: 0.143 AC: 1514 AN: 10606

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7430 AN: 68006

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.128 Hom.: 181

Bravo AF: 0.155

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1703975; hg19: chr8-8577339;