rs566821

Positions:

• chr18-2104792-G-A
• chr18-2104792-G-C

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.619+21408C>T 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 0.865 in 151,016 control chromosomes in the GnomAD database, including 56,836 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 0.87 (56836 hom., cov: 26)
• Consequence: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371956	XR_935087.3	n.271+6852C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639316.2	n.619+21408C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.865 AC: 130569 AN: 150898 Hom.: 56780 Cov.: 26

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.865 AC: 130685 AN: 151016 Hom.: 56836 Cov.: 26 AF XY: 0.870 AC XY: 64115 AN XY: 73684

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.857

Alfa AF: 0.817 Hom.: 63712

Bravo AF: 0.870

Asia WGS AF: 0.941 AC: 3274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566821; hg19: chr18-2104793;