rs10978781

Variant names:

• chr9-96746198-T-C
• rs10978781
• ENST00000653137.4:n.286-27262T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653137.4(ENSG00000224848):​n.286-27262T>C variant causes a intron 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: ENSG00000224848 ENST00000653137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 5 publications found

Genes affected

ENSG00000224848 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653137.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224848	ENST00000653137.4		n.286-27262T>C		intron	N/A
	ENSG00000224848	ENST00000656729.3		n.272+25068T>C		intron	N/A
	ENSG00000224848	ENST00000661289.3		n.472+25068T>C		intron	N/A

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

African (AFR) AF: 0.635 AC: 26325 AN: 41460

American (AMR) AF: 0.0927 AC: 1418 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5160

South Asian (SAS) AF: 0.118 AC: 568 AN: 4824

European-Finnish (FIN) AF: 0.0927 AC: 982 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1145 AN: 68004

Other (OTH) AF: 0.152 AC: 320 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		-0.89

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10978781;

hg19: chr9-99508480;