rs9389835

Variant names:

• chr6-140949523-T-C
• rs9389835
• ENST00000765626.1:n.236+7560T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000765626.1(ENSG00000299692):​n.236+7560T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,024 control chromosomes in the GnomAD database, including 10,784 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 0.37 (10784 hom., cov: 32)
• Consequence: ENSG00000299692 ENST00000765626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96
• Publications: 3 publications found

Genes affected

ENSG00000299692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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
ENSG00000299692	ENST00000765626.1	n.236+7560T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56143 AN: 151906 Hom.: 10786 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.369 AC: 56167 AN: 152024 Hom.: 10784 Cov.: 32 AF XY: 0.361 AC XY: 26825 AN XY: 74302

African (AFR) AF: 0.447 AC: 18510 AN: 41454

American (AMR) AF: 0.279 AC: 4254 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5162

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3541 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25110 AN: 67970

Other (OTH) AF: 0.365 AC: 770 AN: 2112

Alfa AF: 0.370 Hom.: 44548

Bravo AF: 0.370

Asia WGS AF: 0.266 AC: 925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.71
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs9389835; hg19: chr6-141270660;