rs9725031

Variant names:

• chr1-232308709-C-T
• rs9725031
• ENST00000808822.1:n.374+4013G>A

Variant summary

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

The ENST00000808822.1(ENSG00000305110):​n.374+4013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,176 control chromosomes in the GnomAD database, including 1,287 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 0.13 (1287 hom., cov: 32)
• Consequence: ENSG00000305110 ENST00000808822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 3 publications found

Genes affected

ENSG00000305110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808822.1. 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
	ENSG00000305110	ENST00000808822.1		n.374+4013G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19293 AN: 152058 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.127 AC: 19310 AN: 152176 Hom.: 1287 Cov.: 32 AF XY: 0.127 AC XY: 9424 AN XY: 74398

African (AFR) AF: 0.169 AC: 6995 AN: 41508

American (AMR) AF: 0.117 AC: 1783 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3470

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5176

South Asian (SAS) AF: 0.128 AC: 618 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10582

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7685 AN: 68010

Other (OTH) AF: 0.123 AC: 260 AN: 2116

Alfa AF: 0.119 Hom.: 430

Bravo AF: 0.126

Asia WGS AF: 0.129 AC: 447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.55

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: rs9725031;

hg19: chr1-232444455;