rs2894386

Variant names:

• chr10-78742451-C-A
• rs2894386
• ENST00000764443.1:n.444+1647G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-78742451-C-A
• chr10-78742451-C-T

Variant summary

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

The ENST00000764443.1(ENSG00000228683):​n.444+1647G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,182 control chromosomes in the GnomAD database, including 2,343 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 0.17 (2343 hom., cov: 32)
• Consequence: ENSG00000228683 ENST00000764443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 2 publications found

Genes affected

ENSG00000228683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764443.1. 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
	ENSG00000228683	ENST00000764443.1		n.444+1647G>T		intron	N/A
	ENSG00000228683	ENST00000764444.1		n.425+1647G>T		intron	N/A
	ENSG00000228683	ENST00000764445.1		n.76+1647G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26614 AN: 152064 Hom.: 2341 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.175 AC: 26630 AN: 152182 Hom.: 2343 Cov.: 32 AF XY: 0.170 AC XY: 12658 AN XY: 74410

African (AFR) AF: 0.178 AC: 7402 AN: 41498

American (AMR) AF: 0.134 AC: 2044 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.0826 AC: 428 AN: 5180

South Asian (SAS) AF: 0.117 AC: 563 AN: 4824

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13637 AN: 67998

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.192 Hom.: 2275

Bravo AF: 0.176

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.3
DANN	Benign	0.46
PhyloP100		0.058

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: rs2894386;

hg19: chr10-80502208;