rs10510710

chr3-40859859-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412811.1(ENSG00000231873):n.266-2533A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,272 control chromosomes in the GnomAD database, including 449 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 0.066 (449 hom., cov: 32)
• Consequence: ENST00000412811.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377043	XR_007095885.1	n.266-51089A>G		intron_variant, non_coding_transcript_variant
LOC105377043	XR_940766.3	n.266-10025A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412811.1	n.266-2533A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10008 AN: 152154 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0658 AC: 10021 AN: 152272 Hom.: 449 Cov.: 32 AF XY: 0.0634 AC XY: 4723 AN XY: 74464

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0685

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0609 Hom.: 97

Bravo AF: 0.0731

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.58
Dann	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10510710; hg19: chr3-40901350;