rs10460943

Variant names:

• chr3-71623155-C-T
• rs10460943
• ENST00000647725.1:c.-420+66855G>A

Variant summary

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

The ENST00000647725.1(ENSG00000285708):​c.-420+66855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,172 control chromosomes in the GnomAD database, including 3,269 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 0.20 (3269 hom., cov: 32)
• Consequence: ENSG00000285708 ENST00000647725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 2 publications found

Genes affected

ENSG00000285708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285708	ENST00000647725.1	c.-420+66855G>A		intron_variant	Intron 6 of 25			ENSP00000497585.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30524 AN: 152054 Hom.: 3260 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30575 AN: 152172 Hom.: 3269 Cov.: 32 AF XY: 0.200 AC XY: 14881 AN XY: 74396

African (AFR) AF: 0.272 AC: 11295 AN: 41494

American (AMR) AF: 0.247 AC: 3770 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.127 AC: 659 AN: 5176

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11181 AN: 68010

Other (OTH) AF: 0.194 AC: 410 AN: 2112

Alfa AF: 0.178 Hom.: 4267

Bravo AF: 0.212

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.044
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10460943; hg19: chr3-71672306;