rs488101

Positions:

• chr9-117945347-C-T

Variant summary

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

The ENST00000697639.1(ENSG00000284977):​n.1053+97192C>T 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 0.692 in 152,002 control chromosomes in the GnomAD database, including 37,898 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 0.69 (37898 hom., cov: 31)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.1053+97192C>T		intron_variant, non_coding_transcript_variant
	ENST00000697724.1	n.1173-111683C>T		intron_variant, non_coding_transcript_variant
	ENST00000703416.1	n.346+97192C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105087 AN: 151884 Hom.: 37850 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.692 AC: 105191 AN: 152002 Hom.: 37898 Cov.: 31 AF XY: 0.683 AC XY: 50729 AN XY: 74262

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.706

Alfa AF: 0.673 Hom.: 8135

Bravo AF: 0.718

Asia WGS AF: 0.609 AC: 2118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488101; hg19: chr9-120707625; COSMIC: COSV60397318;