rs2928464

Variant names:

• chr10-57336182-C-A
• rs2928464
• ENST00000837137.1:n.484G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-57336182-C-A
• chr10-57336182-C-G
• chr10-57336182-C-T

Variant summary

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

The ENST00000837137.1(ENSG00000308896):​n.484G>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 0.138 in 152,046 control chromosomes in the GnomAD database, including 2,658 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 0.14 (2658 hom., cov: 32)
• Consequence: ENSG00000308896 ENST00000837137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 6 publications found

Genes affected

ENSG00000308896 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837137.1. 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
	ENSG00000308896	ENST00000837137.1		n.484G>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20974 AN: 151926 Hom.: 2653 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0395

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.138 AC: 21022 AN: 152046 Hom.: 2658 Cov.: 32 AF XY: 0.139 AC XY: 10295 AN XY: 74308

African (AFR) AF: 0.330 AC: 13649 AN: 41386

American (AMR) AF: 0.200 AC: 3053 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 478 AN: 5168

South Asian (SAS) AF: 0.0808 AC: 390 AN: 4824

European-Finnish (FIN) AF: 0.0292 AC: 310 AN: 10606

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0395 AC: 2688 AN: 68004

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.0458 Hom.: 169

Bravo AF: 0.160

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.33
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: rs2928464;

hg19: chr10-59095942;