rs10978781

Positions:

• chr9-96746198-T-C
• chr9-96746198-T-G

Variant summary

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

The ENST00000661289.3(ENSG00000224848):​n.472+25068T>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 0.215 in 152,134 control chromosomes in the GnomAD database, including 8,976 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 0.21 (8976 hom., cov: 32)
• Consequence: ENST00000661289.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

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 = 0.629 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
	ENST00000661289.3	n.472+25068T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32583 AN: 152016 Hom.: 8926 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.215 AC: 32679 AN: 152134 Hom.: 8976 Cov.: 32 AF XY: 0.216 AC XY: 16037 AN XY: 74374

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.0927

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0927

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.152

Alfa AF: 0.145 Hom.: 1374

Bravo AF: 0.235

Asia WGS AF: 0.209 AC: 727 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	2.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10978781; hg19: chr9-99508480;