rs1509937

Variant names:

• chr10-65296147-A-G
• rs1509937
• ENST00000648274.1:n.105+10034A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-65296147-A-G
• chr10-65296147-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648274.1(ENSG00000235356):​n.105+10034A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,774 control chromosomes in the GnomAD database, including 6,854 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 0.29 (6854 hom., cov: 31)
• Consequence: ENSG00000235356 ENST00000648274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

ENSG00000235356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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
ENSG00000235356	ENST00000648274.1	n.105+10034A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44051 AN: 151658 Hom.: 6848 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.317

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 44065 AN: 151774 Hom.: 6854 Cov.: 31 AF XY: 0.288 AC XY: 21356 AN XY: 74170

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.299

Alfa AF: 0.331 Hom.: 17054

Bravo AF: 0.282

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509937; hg19: chr10-67055905;