rs1509937

Positions:

• 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, non coding transcript 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: ENST00000648274.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648274.1	n.105+10034A>G		intron_variant, non_coding_transcript_variant

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;