rs985492

Variant names:

• chr18-31731071-G-A
• rs985492
• ENST00000693320.1:n.922+5750G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-31731071-G-A
• chr18-31731071-G-C
• chr18-31731071-G-T

Variant summary

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

The ENST00000693320.1(LRRC37A7P):​n.922+5750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,980 control chromosomes in the GnomAD database, including 22,055 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 (22055 hom., cov: 32)
• Consequence: LRRC37A7P ENST00000693320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

LRRC37A7P (HGNC:43792): (leucine rich repeat containing 37 member A7, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC37A7P	ENST00000693320.1	n.922+5750G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81645 AN: 151862 Hom.: 22035 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81717 AN: 151980 Hom.: 22055 Cov.: 32 AF XY: 0.540 AC XY: 40102 AN XY: 74264

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.512

Alfa AF: 0.520 Hom.: 46167

Bravo AF: 0.535

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985492; hg19: chr18-29311034;