rs9486902

Positions:

• chr6-108556849-C-T

Variant summary

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

The ENST00000659932.1(ENSG00000287044):​n.123+1315G>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 0.177 in 152,138 control chromosomes in the GnomAD database, including 2,609 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 0.18 (2609 hom., cov: 32)
• Consequence: ENST00000659932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901372	XR_007059700.1	n.343+1315G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659932.1	n.123+1315G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26974 AN: 152020 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.177 AC: 26992 AN: 152138 Hom.: 2609 Cov.: 32 AF XY: 0.172 AC XY: 12812 AN XY: 74380

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.0579

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.185

Alfa AF: 0.169 Hom.: 3707

Bravo AF: 0.190

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9486902; hg19: chr6-108878052; COSMIC: COSV59627004;