rs10983777

Positions:

• chr9-117763702-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697639.1(ENSG00000284977):​n.127+2253C>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 0.135 in 152,196 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 32)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376244	XR_007061905.1	n.1993+2253C>G		intron_variant, non_coding_transcript_variant
LOC105376244	XR_001746916.2	n.1234+2253C>G		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061906.1	n.1234+2253C>G		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061907.1	n.1993+2253C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000697639.1	n.127+2253C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20517 AN: 152078 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.135 AC: 20516 AN: 152196 Hom.: 1727 Cov.: 32 AF XY: 0.134 AC XY: 9954 AN XY: 74388

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.137

Alfa AF: 0.160 Hom.: 263

Bravo AF: 0.127

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10983777; hg19: chr9-120525980; COSMIC: COSV60396950;