9-104928452-G-A

Position:

• chr9-104928452-G-A

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-330G>A 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 0.175 in 152,066 control chromosomes in the GnomAD database, including 2,894 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 0.18 (2894 hom., cov: 33)
• Consequence: ENST00000435915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376196	XR_930204.3	n.1122+542G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435915.1	n.359-330G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26628 AN: 151946 Hom.: 2900 Cov.: 33

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.175 AC: 26627 AN: 152066 Hom.: 2894 Cov.: 33 AF XY: 0.180 AC XY: 13409 AN XY: 74318

Gnomad4 AFR AF: 0.0558

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.185

Alfa AF: 0.164 Hom.: 377

Bravo AF: 0.163

Asia WGS AF: 0.293 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.036
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246298; hg19: chr9-107690733;