rs9951407

Positions:

• chr18-35955907-T-C

Variant summary

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

The ENST00000589074.1(ENSG00000267627):​n.375-3870A>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 0.1 in 152,218 control chromosomes in the GnomAD database, including 882 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 0.10 (882 hom., cov: 32)
• Consequence: ENST00000589074.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372066	XR_935379.4	n.422-3870A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000589074.1	n.375-3870A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000586982.5	n.97-3108A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15203 AN: 152100 Hom.: 881 Cov.: 32

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.0697

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.100 AC: 15217 AN: 152218 Hom.: 882 Cov.: 32 AF XY: 0.0981 AC XY: 7302 AN XY: 74420

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.117 Hom.: 1574

Bravo AF: 0.0962

Asia WGS AF: 0.0520 AC: 180 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.8
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9951407; hg19: chr18-33535870;