rs9957708

Positions:

• chr18-27799426-A-G
• chr18-27799426-A-T

Variant summary

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

The XR_935323.3(LOC105372042):​n.696-3495A>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 0.543 in 152,012 control chromosomes in the GnomAD database, including 24,622 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 0.54 (24622 hom., cov: 33)
• Consequence: LOC105372042 XR_935323.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

LOC105372042 (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 (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372042	XR_935323.3	n.696-3495A>G		intron_variant, non_coding_transcript_variant
LOC105372042	XR_935324.3	n.628-3495A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82511 AN: 151896 Hom.: 24616 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.543 AC: 82531 AN: 152012 Hom.: 24622 Cov.: 33 AF XY: 0.548 AC XY: 40701 AN XY: 74306

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.557

Alfa AF: 0.598 Hom.: 4804

Bravo AF: 0.526

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9957708; hg19: chr18-25379390;