rs9355741

Variant names:

• chr6-159608976-G-A
• rs9355741
• ENST00000656085.1:n.42+53610C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656085.1(ENSG00000286533):​n.42+53610C>T variant causes a intron 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: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 9 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286533	ENST00000656085.1	n.42+53610C>T		intron_variant	Intron 1 of 1
ENSG00000286533	ENST00000794978.1	n.186-13772C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.202 AC: 8399 AN: 41478

American (AMR) AF: 0.375 AC: 5728 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1573 AN: 5164

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 4029 AN: 10572

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22617 AN: 67970

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.321 Hom.: 36132

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
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs9355741; hg19: chr6-160030008;