rs10081672

Variant names:

• chr9-35155911-A-G
• rs10081672
• ENST00000836210.1:n.422+185T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-35155911-A-G
• chr9-35155911-A-T

Variant summary

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

The ENST00000836210.1(ENSG00000308740):​n.422+185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,010 control chromosomes in the GnomAD database, including 11,503 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 0.38 (11503 hom., cov: 31)
• Consequence: ENSG00000308740 ENST00000836210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 8 publications found

Genes affected

ENSG00000308740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902147	XR_007061468.1	n.339+185T>C		intron_variant	Intron 1 of 1
LOC124902147	XR_007061469.1	n.339+185T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308740	ENST00000836210.1	n.422+185T>C		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836211.1	n.722+185T>C		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836212.1	n.962+185T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57615 AN: 151892 Hom.: 11486 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.379 AC: 57677 AN: 152010 Hom.: 11503 Cov.: 31 AF XY: 0.374 AC XY: 27790 AN XY: 74316

African (AFR) AF: 0.365 AC: 15139 AN: 41440

American (AMR) AF: 0.433 AC: 6613 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3468

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5184

South Asian (SAS) AF: 0.181 AC: 874 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4919 AN: 10566

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27580 AN: 67938

Other (OTH) AF: 0.383 AC: 809 AN: 2112

Alfa AF: 0.368 Hom.: 3569

Bravo AF: 0.376

Asia WGS AF: 0.136 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10081672; hg19: chr9-35155908;