rs2675677

Variant names:

• chr10-73888491-C-A
• rs2675677
• ENST00000746715.1:n.464G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-73888491-C-A
• chr10-73888491-C-G
• chr10-73888491-C-T

Variant summary

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

The ENST00000746715.1(ENSG00000297271):​n.464G>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 0.715 in 151,986 control chromosomes in the GnomAD database, including 39,505 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 0.71 (39505 hom., cov: 32)
• Consequence: ENSG00000297271 ENST00000746715.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 9 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902454	XR_007062196.1	n.416G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297271	ENST00000746715.1	n.464G>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000297271	ENST00000746716.1	n.465G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297271	ENST00000746717.1	n.258G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297292	ENST00000746853.1	n.-231C>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108597 AN: 151868 Hom.: 39479 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.715 AC: 108657 AN: 151986 Hom.: 39505 Cov.: 32 AF XY: 0.706 AC XY: 52380 AN XY: 74238

African (AFR) AF: 0.763 AC: 31628 AN: 41474

American (AMR) AF: 0.589 AC: 8986 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2477 AN: 5150

South Asian (SAS) AF: 0.580 AC: 2783 AN: 4796

European-Finnish (FIN) AF: 0.624 AC: 6576 AN: 10542

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50663 AN: 67982

Other (OTH) AF: 0.754 AC: 1595 AN: 2114

Alfa AF: 0.739 Hom.: 130925

Bravo AF: 0.717

Asia WGS AF: 0.508 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2675677; hg19: chr10-75648249;