rs1031830

Positions:

• chr18-55797536-G-A
• chr18-55797536-G-T

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.634+5638G>A 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 0.581 in 152,054 control chromosomes in the GnomAD database, including 27,817 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 0.58 (27817 hom., cov: 32)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.806+5638G>A		intron_variant, non_coding_transcript_variant
LOC105372130	XR_007066383.1	n.1501+5638G>A		intron_variant, non_coding_transcript_variant
LOC105372130	XR_935487.3	n.1572+5638G>A		intron_variant, non_coding_transcript_variant
LOC105372130	XR_935488.3	n.1390+8775G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654829.1	n.634+5638G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88308 AN: 151936 Hom.: 27794 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.581 AC: 88372 AN: 152054 Hom.: 27817 Cov.: 32 AF XY: 0.587 AC XY: 43611 AN XY: 74320

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.625

Alfa AF: 0.623 Hom.: 3819

Bravo AF: 0.573

Asia WGS AF: 0.596 AC: 2070 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	0.49
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031830; hg19: chr18-53464767;