9-91486800-T-C

Variant names:

• chr9-91486800-T-C
• rs4744055
• ENST00000730195.1:n.256+232A>G

Variant summary

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

The ENST00000730195.1(ENSG00000295449):​n.256+232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,110 control chromosomes in the GnomAD database, including 21,326 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 0.49 (21326 hom., cov: 32)
• Consequence: ENSG00000295449 ENST00000730195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 7 publications found

Genes affected

ENSG00000295449 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295449	ENST00000730195.1	n.256+232A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74066 AN: 151992 Hom.: 21299 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.487 AC: 74142 AN: 152110 Hom.: 21326 Cov.: 32 AF XY: 0.486 AC XY: 36153 AN XY: 74348

African (AFR) AF: 0.798 AC: 33098 AN: 41472

American (AMR) AF: 0.332 AC: 5074 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3564 AN: 5174

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4824

European-Finnish (FIN) AF: 0.384 AC: 4064 AN: 10570

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23256 AN: 67990

Other (OTH) AF: 0.461 AC: 974 AN: 2112

Alfa AF: 0.377 Hom.: 20278

Bravo AF: 0.500

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.39
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4744055; hg19: chr9-94249082; COSMIC: COSV60378271;