rs2501677

Positions:

• chr10-6904790-A-T

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.568+30323T>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 0.0693 in 152,234 control chromosomes in the GnomAD database, including 457 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 0.069 (457 hom., cov: 32)
• Consequence: ENST00000664549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376387	XR_007062046.1	n.851+15639T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664549.1	n.568+30323T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10538 AN: 152116 Hom.: 457 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0693 AC: 10550 AN: 152234 Hom.: 457 Cov.: 32 AF XY: 0.0681 AC XY: 5069 AN XY: 74428

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0724

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0860 Hom.: 337

Bravo AF: 0.0695

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2501677; hg19: chr10-6946752;