rs10460943

chr3-71623155-C-T

Variant summary

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

The ENST00000613067.1(ENSG00000277855):n.58-4486C>T 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 0.201 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: ENST00000613067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000613067.1	n.58-4486C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.194

Alfa AF: 0.174 Hom.: 3202

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10460943; hg19: chr3-71672306;