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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765951.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299739	ENST00000765951.1		n.155-33040T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1335510;

hg19: chr9-21757803;