rs10511254

chr3-106203747-G-A

Variant summary

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

The ENST00000667697.1(ENSG00000287421):n.254+1164G>A 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 0.172 in 145,300 control chromosomes in the GnomAD database, including 2,563 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 0.17 (2563 hom., cov: 29)
• Consequence: ENST00000667697.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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
	ENST00000667697.1	n.254+1164G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 25011 AN: 145168 Hom.: 2560 Cov.: 29

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.172 AC: 25021 AN: 145300 Hom.: 2563 Cov.: 29 AF XY: 0.174 AC XY: 12272 AN XY: 70676

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.174

Alfa AF: 0.189 Hom.: 509

Bravo AF: 0.159

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511254; hg19: chr3-105922594;