rs972900

Variant names:

• chr18-37755682-T-C
• rs972900
• XM_047437984.1:c.111+16678A>G

Variant summary

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

The XM_047437984.1(LOC105372073):​c.111+16678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,128 control chromosomes in the GnomAD database, including 7,899 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 0.32 (7899 hom., cov: 33)
• Consequence: LOC105372073 XM_047437984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

Genes affected

LOC105372073 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372073	XM_047437984.1	c.111+16678A>G		intron_variant	Intron 2 of 2		XP_047293940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285940	ENST00000649194.1	n.1453+817T>C		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47954 AN: 152010 Hom.: 7887 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47988 AN: 152128 Hom.: 7899 Cov.: 33 AF XY: 0.323 AC XY: 24022 AN XY: 74338

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.297

Alfa AF: 0.310 Hom.: 15516

Bravo AF: 0.312

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972900; hg19: chr18-35335646;