rs10983837

Positions:

• chr9-117936537-C-A
• chr9-117936537-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000697639.1(ENSG00000284977):​n.1053+88382C>A 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 0.0253 in 151,904 control chromosomes in the GnomAD database, including 71 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 0.025 (71 hom., cov: 31)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0253 (3836/151904) while in subpopulation NFE AF= 0.0373 (2537/67966). AF 95% confidence interval is 0.0361. There are 71 homozygotes in gnomad4. There are 1835 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 71 gene

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
	ENST00000697639.1	n.1053+88382C>A		intron_variant, non_coding_transcript_variant
	ENST00000697724.1	n.1173-120493C>A		intron_variant, non_coding_transcript_variant
	ENST00000703416.1	n.346+88382C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3832 AN: 151788 Hom.: 70 Cov.: 31

Gnomad AFR AF: 0.00649

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0322

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

GnomAD4 genome AF: 0.0253 AC: 3836 AN: 151904 Hom.: 71 Cov.: 31 AF XY: 0.0247 AC XY: 1835 AN XY: 74244

Gnomad4 AFR AF: 0.00647

Gnomad4 AMR AF: 0.0257

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0208

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0319

Alfa AF: 0.0222 Hom.: 11

Bravo AF: 0.0245

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10983837; hg19: chr9-120698815;