rs2675675

Variant names:

• chr10-73889290-G-A
• rs2675675
• ENST00000746715.1:n.222C>T

Variant summary

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

The ENST00000746715.1(ENSG00000297271):​n.222C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,084 control chromosomes in the GnomAD database, including 40,423 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 0.72 (40423 hom., cov: 31)
• Consequence: ENSG00000297271 ENST00000746715.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 3 publications found

Genes affected

ENSG00000297271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902454	XR_007062196.1	n.174C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297271	ENST00000746715.1	n.222C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000297271	ENST00000746716.1	n.223C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000297271	ENST00000746717.1	n.79+100C>T		intron_variant	Intron 1 of 1
ENSG00000297292	ENST00000746853.1	n.276+293G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109897 AN: 151968 Hom.: 40400 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.723 AC: 109953 AN: 152084 Hom.: 40423 Cov.: 31 AF XY: 0.713 AC XY: 53037 AN XY: 74358

African (AFR) AF: 0.765 AC: 31750 AN: 41490

American (AMR) AF: 0.595 AC: 9094 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3148 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2475 AN: 5142

South Asian (SAS) AF: 0.605 AC: 2918 AN: 4822

European-Finnish (FIN) AF: 0.630 AC: 6663 AN: 10584

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51406 AN: 67978

Other (OTH) AF: 0.767 AC: 1620 AN: 2112

Alfa AF: 0.729 Hom.: 13825

Bravo AF: 0.724

Asia WGS AF: 0.518 AC: 1805 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.42
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2675675; hg19: chr10-75649048;