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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377043	XR_007095886.1	n.57+537A>G		intron_variant	Intron 1 of 3
LOC124909370	XR_007095888.1	n.250+300T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231873	ENST00000665970.1	n.57+537A>G		intron_variant	Intron 1 of 3
ENSG00000295859	ENST00000733244.1	n.285+300T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs10510714; hg19: chr3-40761943;