rs2153535

Positions:

• chr6-8369446-C-G
• chr6-8369446-C-T

Variant summary

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

The ENST00000670476.1(ENSG00000234763):​n.228+9293G>C 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 0.401 in 151,870 control chromosomes in the GnomAD database, including 12,899 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 0.40 (12899 hom., cov: 31)
• Consequence: ENST00000670476.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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
	ENST00000670476.1	n.228+9293G>C		intron_variant, non_coding_transcript_variant
	ENST00000651914.1	n.160-1030G>C		intron_variant, non_coding_transcript_variant
	ENST00000655767.1	n.229-6614G>C		intron_variant, non_coding_transcript_variant
	ENST00000661402.1	n.424+19314G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60811 AN: 151752 Hom.: 12893 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.401 AC: 60835 AN: 151870 Hom.: 12899 Cov.: 31 AF XY: 0.392 AC XY: 29074 AN XY: 74214

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.381

Alfa AF: 0.448 Hom.: 1935

Bravo AF: 0.393

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2153535; hg19: chr6-8369679;