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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1	n.483+8799G>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308896	ENST00000837137.1	n.484G>T		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2928464; hg19: chr10-59095942;