rs9355741

chr6-159608976-G-A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):n.42+53610C>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 0.304 in 152,052 control chromosomes in the GnomAD database, including 7,501 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 0.30 (7501 hom., cov: 32)
• Consequence: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.367 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
	ENST00000656085.1	n.42+53610C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46221 AN: 151934 Hom.: 7495 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.304 AC: 46226 AN: 152052 Hom.: 7501 Cov.: 32 AF XY: 0.309 AC XY: 22978 AN XY: 74334

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.325

Alfa AF: 0.326 Hom.: 18493

Bravo AF: 0.297

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.3
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: rs9355741; hg19: chr6-160030008;