rs7670758

Variant names:

• chr4-144590723-A-G
• rs7670758
• ENST00000649263.1:n.328-174745T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-174745T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,050 control chromosomes in the GnomAD database, including 36,746 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 0.68 (36746 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.26
• Publications: 11 publications found

Genes affected

ENSG00000285713 (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 (AFR) allele frequency at 95% confidence interval = 0.861 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
ENSG00000285713	ENST00000649263.1	n.328-174745T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+164434T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103675 AN: 151932 Hom.: 36691 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.683 AC: 103796 AN: 152050 Hom.: 36746 Cov.: 32 AF XY: 0.688 AC XY: 51156 AN XY: 74316

African (AFR) AF: 0.868 AC: 36019 AN: 41490

American (AMR) AF: 0.651 AC: 9941 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1885 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3239 AN: 5148

South Asian (SAS) AF: 0.848 AC: 4084 AN: 4816

European-Finnish (FIN) AF: 0.680 AC: 7182 AN: 10558

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39463 AN: 67974

Other (OTH) AF: 0.624 AC: 1316 AN: 2110

Alfa AF: 0.619 Hom.: 90856

Bravo AF: 0.677

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.51
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs7670758; hg19: chr4-145511875;