rs2246293

chr9-104928557-C-Gchr9-104928557-C-T

Variant summary

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

The ENST00000435915.1(ENSG00000226334):n.359-225C>G 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 0.478 in 152,154 control chromosomes in the GnomAD database, including 17,651 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 0.48 (17651 hom., cov: 34)
• Consequence: ENST00000435915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376196	XR_930204.3	n.1122+647C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435915.1	n.359-225C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72769 AN: 152036 Hom.: 17647 Cov.: 34

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.478 AC: 72804 AN: 152154 Hom.: 17651 Cov.: 34 AF XY: 0.483 AC XY: 35965 AN XY: 74386

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.483

Alfa AF: 0.347 Hom.: 929

Bravo AF: 0.474

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.49
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246293; hg19: chr9-107690838;