3-40720452-A-G

Variant names:

• chr3-40720452-A-G
• rs10510714
• ENST00000665970.1:n.57+537A>G

Variant summary

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

The ENST00000665970.1(ENSG00000231873):​n.57+537A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,332 control chromosomes in the GnomAD database, including 62 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 0.025 (62 hom., cov: 32)
• Consequence: ENSG00000231873 ENST00000665970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 1 publications found

Genes affected

ENSG00000231873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665970.1. 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
	ENSG00000231873	ENST00000665970.1		n.57+537A>G		intron	N/A
	ENSG00000295859	ENST00000733244.1		n.285+300T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3837 AN: 152214 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00931

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0252 AC: 3843 AN: 152332 Hom.: 62 Cov.: 32 AF XY: 0.0271 AC XY: 2020 AN XY: 74486

African (AFR) AF: 0.00945 AC: 393 AN: 41588

American (AMR) AF: 0.0453 AC: 694 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.0632 AC: 327 AN: 5178

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4818

European-Finnish (FIN) AF: 0.0386 AC: 410 AN: 10618

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1730 AN: 68028

Other (OTH) AF: 0.0170 AC: 36 AN: 2116

Alfa AF: 0.0230 Hom.: 60

Bravo AF: 0.0246

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.42
PhyloP100		-0.76

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: rs10510714;

hg19: chr3-40761943;