rs6597703

Variant names:

• chr10-125408462-A-C
• rs6597703
• ENST00000753056.1:n.309-4747A>C

Variant summary

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

The ENST00000753056.1(ENSG00000298113):​n.309-4747A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,182 control chromosomes in the GnomAD database, including 4,184 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 0.23 (4184 hom., cov: 32)
• Consequence: ENSG00000298113 ENST00000753056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802
• Publications: 3 publications found

Genes affected

ENSG00000298113 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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
ENSG00000298113	ENST00000753056.1	n.309-4747A>C		intron_variant	Intron 2 of 2
ENSG00000298113	ENST00000753057.1	n.249-4747A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35009 AN: 152064 Hom.: 4174 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.230 AC: 35058 AN: 152182 Hom.: 4184 Cov.: 32 AF XY: 0.229 AC XY: 17056 AN XY: 74398

African (AFR) AF: 0.293 AC: 12140 AN: 41500

American (AMR) AF: 0.166 AC: 2536 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3472

East Asian (EAS) AF: 0.104 AC: 538 AN: 5190

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4820

European-Finnish (FIN) AF: 0.246 AC: 2607 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14670 AN: 68012

Other (OTH) AF: 0.213 AC: 450 AN: 2114

Alfa AF: 0.222 Hom.: 10168

Bravo AF: 0.226

Asia WGS AF: 0.160 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.46
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs6597703; hg19: chr10-127097031;