9-2270503-T-C

Variant names:

• chr9-2270503-T-C
• rs7024139
• ENST00000816240.1:n.220-2972T>C

Variant summary

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

The ENST00000816240.1(ENSG00000306202):​n.220-2972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,892 control chromosomes in the GnomAD database, including 22,644 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 0.54 (22644 hom., cov: 31)
• Consequence: ENSG00000306202 ENST00000816240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 1 publications found

Genes affected

ENSG00000306202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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
ENSG00000306202	ENST00000816240.1	n.220-2972T>C		intron_variant	Intron 2 of 2
ENSG00000306202	ENST00000816241.1	n.316-2972T>C		intron_variant	Intron 2 of 2
ENSG00000306202	ENST00000816242.1	n.392-3373T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81998 AN: 151774 Hom.: 22614 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.540 AC: 82086 AN: 151892 Hom.: 22644 Cov.: 31 AF XY: 0.546 AC XY: 40500 AN XY: 74206

African (AFR) AF: 0.582 AC: 24088 AN: 41396

American (AMR) AF: 0.552 AC: 8422 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3468

East Asian (EAS) AF: 0.877 AC: 4532 AN: 5170

South Asian (SAS) AF: 0.593 AC: 2848 AN: 4800

European-Finnish (FIN) AF: 0.523 AC: 5517 AN: 10548

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32767 AN: 67926

Other (OTH) AF: 0.544 AC: 1146 AN: 2108

Alfa AF: 0.499 Hom.: 10596

Bravo AF: 0.544

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.19
DANN	Benign	0.73
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7024139; hg19: chr9-2270503; COSMIC: COSV69442808;