rs9351685

Variant names:

• chr6-67910027-T-A
• rs9351685
• ENST00000653528.1:n.131+20920T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-67910027-T-A
• chr6-67910027-T-G

Variant summary

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

The ENST00000653528.1(ENSG00000286680):​n.131+20920T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 150,546 control chromosomes in the GnomAD database, including 259 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 0.044 (259 hom., cov: 29)
• Consequence: ENSG00000286680 ENST00000653528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 1 publications found

Genes affected

ENSG00000286680 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377845	XR_942662.1	n.909-11424T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286680	ENST00000653528.1	n.131+20920T>A		intron_variant	Intron 1 of 3
ENSG00000286680	ENST00000661401.1	n.121-11424T>A		intron_variant	Intron 2 of 3
ENSG00000286680	ENST00000718119.1	n.154-11424T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0444 AC: 6675 AN: 150446 Hom.: 255 Cov.: 29

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0495

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

GnomAD4 genome AF: 0.0444 AC: 6688 AN: 150546 Hom.: 259 Cov.: 29 AF XY: 0.0451 AC XY: 3315 AN XY: 73506

African (AFR) AF: 0.0113 AC: 461 AN: 40966

American (AMR) AF: 0.0967 AC: 1452 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3468

East Asian (EAS) AF: 0.183 AC: 927 AN: 5056

South Asian (SAS) AF: 0.0423 AC: 201 AN: 4754

European-Finnish (FIN) AF: 0.0222 AC: 230 AN: 10372

Middle Eastern (MID) AF: 0.0379 AC: 11 AN: 290

European-Non Finnish (NFE) AF: 0.0475 AC: 3212 AN: 67642

Other (OTH) AF: 0.0495 AC: 103 AN: 2080

Alfa AF: 0.0427 Hom.: 21

Bravo AF: 0.0515

Asia WGS AF: 0.0950 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.20
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9351685; hg19: chr6-68619919; COSMIC: COSV70884303;