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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746715.1. 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
	ENSG00000297271	ENST00000746715.1		n.464G>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000297271	ENST00000746716.1		n.465G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297271	ENST00000746717.1		n.258G>T		non_coding_transcript_exon	Exon 2 of 2

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 v4.9

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

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

Other links and lift over

dbSNP: rs2675677;

hg19: chr10-75648249;