rs1800976

chr9-104928428-C-G

Variant summary

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

The ENST00000435915.1(ENSG00000226334):n.359-354C>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 0.475 in 151,554 control chromosomes in the GnomAD database, including 17,286 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 0.47 (17286 hom., cov: 31)
• Consequence: ENST00000435915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376196	XR_930204.3	n.1122+518C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435915.1	n.359-354C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71931 AN: 151436 Hom.: 17279 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.475 AC: 71970 AN: 151554 Hom.: 17286 Cov.: 31 AF XY: 0.480 AC XY: 35506 AN XY: 74020

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.479

Alfa AF: 0.463 Hom.: 2020

Bravo AF: 0.472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800976; hg19: chr9-107690709;