rs1335510

Variant names:

• chr9-21757804-T-G
• rs1335510
• ENST00000765951.1:n.155-33040T>G

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.155-33040T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,982 control chromosomes in the GnomAD database, including 9,473 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 0.32 (9473 hom., cov: 32)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 16 publications found

Genes affected

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987026	XR_001746563.3	n.163+10021A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299739	ENST00000765951.1	n.155-33040T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49120 AN: 151864 Hom.: 9467 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.323 AC: 49143 AN: 151982 Hom.: 9473 Cov.: 32 AF XY: 0.323 AC XY: 23986 AN XY: 74250

African (AFR) AF: 0.104 AC: 4337 AN: 41522

American (AMR) AF: 0.386 AC: 5894 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1320 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2217 AN: 5148

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4810

European-Finnish (FIN) AF: 0.418 AC: 4409 AN: 10542

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28696 AN: 67920

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.389 Hom.: 6834

Bravo AF: 0.315

Asia WGS AF: 0.317 AC: 1099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.74
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1335510; hg19: chr9-21757803;