rs1821970

Positions:

• chr4-177220387-T-G

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.301+100A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,278 control chromosomes in the GnomAD database, including 1,293 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 0.11 (1293 hom., cov: 33)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377557	XR_001741925.2	n.423+100A>C		intron_variant
LOC105377557	XR_007058379.1	n.*21A>C		downstream_gene_variant
LOC105377557	XR_007058380.1	n.*21A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287544	ENST00000656694.1	n.301+100A>C		intron_variant
ENSG00000287544	ENST00000662794.1	n.374+100A>C		intron_variant
ENSG00000287544	ENST00000667713.1	n.396+100A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17278 AN: 152160 Hom.: 1296 Cov.: 33

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.113 AC: 17266 AN: 152278 Hom.: 1293 Cov.: 33 AF XY: 0.117 AC XY: 8697 AN XY: 74460

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.0783

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.102

Alfa AF: 0.109 Hom.: 119

Bravo AF: 0.105

Asia WGS AF: 0.256 AC: 888 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1821970; hg19: chr4-178141541;