rs1387837

Variant names:

• chr10-18714164-G-A
• rs1387837
• ENST00000654305.2:n.103+3803G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-18714164-G-A
• chr10-18714164-G-C
• chr10-18714164-G-T

Variant summary

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

The ENST00000654305.2(ENSG00000234244):​n.103+3803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,872 control chromosomes in the GnomAD database, including 24,860 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 0.56 (24860 hom., cov: 31)
• Consequence: ENSG00000234244 ENST00000654305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 3 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654305.2. 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
	ENSG00000234244	ENST00000654305.2		n.103+3803G>A		intron	N/A
	ENSG00000234244	ENST00000654415.1		n.78+3803G>A		intron	N/A
	ENSG00000234244	ENST00000723466.1		n.53+3803G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85472 AN: 151754 Hom.: 24823 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.563 AC: 85559 AN: 151872 Hom.: 24860 Cov.: 31 AF XY: 0.557 AC XY: 41358 AN XY: 74230

African (AFR) AF: 0.717 AC: 29713 AN: 41428

American (AMR) AF: 0.543 AC: 8284 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1524 AN: 3458

East Asian (EAS) AF: 0.549 AC: 2842 AN: 5176

South Asian (SAS) AF: 0.376 AC: 1802 AN: 4792

European-Finnish (FIN) AF: 0.478 AC: 5028 AN: 10514

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34512 AN: 67932

Other (OTH) AF: 0.513 AC: 1083 AN: 2110

Alfa AF: 0.511 Hom.: 58330

Bravo AF: 0.582

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.2
DANN	Benign	0.65
PhyloP100		0.27

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: rs1387837;

hg19: chr10-19003093;