rs2736930

chr10-122451496-A-G

Variant summary

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

The ENST00000650300.1(ENSG00000285955):n.1852+6999T>C 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 0.116 in 151,166 control chromosomes in the GnomAD database, including 1,404 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 0.12 (1404 hom., cov: 32)
• Consequence: ENST00000650300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378525	XR_946382.3	n.1875-557T>C		intron_variant, non_coding_transcript_variant
LOC105378525	XR_946383.3	n.1853-557T>C		intron_variant, non_coding_transcript_variant
LOC105378525	XR_946384.3	n.1602-557T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650300.1	n.1852+6999T>C		intron_variant, non_coding_transcript_variant
	ENST00000647969.1	n.183-587T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17514 AN: 151052 Hom.: 1403 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.000613

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.116 AC: 17514 AN: 151166 Hom.: 1404 Cov.: 32 AF XY: 0.113 AC XY: 8342 AN XY: 73806

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.000615

Gnomad4 SAS AF: 0.0338

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.129

Alfa AF: 0.141 Hom.: 220

Bravo AF: 0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736930; hg19: chr10-124211012;