rs9288786

chr3-104555628-T-G

Variant summary

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

The XR_007096271.1(LOC105374021):n.208+238A>C 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 0.0857 in 152,148 control chromosomes in the GnomAD database, including 1,326 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 0.086 (1326 hom., cov: 32)
• Consequence: LOC105374021 XR_007096271.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

Genes affected

LOC105374021 (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 (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374021	XR_007096271.1	n.208+238A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13023 AN: 152030 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0857 AC: 13035 AN: 152148 Hom.: 1326 Cov.: 32 AF XY: 0.0852 AC XY: 6334 AN XY: 74370

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0388 Hom.: 168

Bravo AF: 0.0946

Asia WGS AF: 0.0450 AC: 157 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	9.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288786; hg19: chr3-104274472;