rs7009110

Variant names:

• chr8-80379644-T-C
• rs7009110
• ENST00000644465.1:n.254-69053T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000644465.1(ENSG00000253238):​n.254-69053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,080 control chromosomes in the GnomAD database, including 22,368 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 0.53 (22368 hom., cov: 32)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 31 publications found

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644465.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253238	ENST00000644465.1		n.254-69053T>C		intron	N/A
	ENSG00000253238	ENST00000656157.2		n.285+90642T>C		intron	N/A
	ENSG00000253238	ENST00000656811.1		n.252-23092T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80219 AN: 151962 Hom.: 22370 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.528 AC: 80235 AN: 152080 Hom.: 22368 Cov.: 32 AF XY: 0.529 AC XY: 39296 AN XY: 74344

African (AFR) AF: 0.349 AC: 14485 AN: 41478

American (AMR) AF: 0.547 AC: 8350 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1868 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2293 AN: 5182

South Asian (SAS) AF: 0.527 AC: 2537 AN: 4818

European-Finnish (FIN) AF: 0.664 AC: 7024 AN: 10582

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41714 AN: 67960

Other (OTH) AF: 0.542 AC: 1146 AN: 2114

Alfa AF: 0.571 Hom.: 37015

Bravo AF: 0.507

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7009110;

hg19: chr8-81291879;