rs9959302

Positions:

• chr18-38482221-T-A
• chr18-38482221-T-C
• chr18-38482221-T-G

Variant summary

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

The XR_935392.1(LOC105372074):​n.204+7860A>T 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 0.422 in 152,028 control chromosomes in the GnomAD database, including 14,503 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 0.42 (14503 hom., cov: 32)
• Consequence: LOC105372074 XR_935392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

LOC105372074 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372074	XR_935392.1	n.204+7860A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64142 AN: 151910 Hom.: 14481 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.422 AC: 64207 AN: 152028 Hom.: 14503 Cov.: 32 AF XY: 0.419 AC XY: 31137 AN XY: 74310

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.434

Alfa AF: 0.365 Hom.: 1366

Bravo AF: 0.443

Asia WGS AF: 0.490 AC: 1703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9959302; hg19: chr18-36062185;