rs3806237

chr1-100250226-T-C

Variant summary

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

The ENST00000648283.1(ENSG00000285530):n.600T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 152,314 control chromosomes in the GnomAD database, including 86 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 0.025 (86 hom., cov: 33)
• Consequence: ENST00000648283.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

Genes affected

(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 = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648283.1	n.600T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.0255 AC: 3874 AN: 152196 Hom.: 88 Cov.: 33

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00776

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0254 AC: 3865 AN: 152314 Hom.: 86 Cov.: 33 AF XY: 0.0260 AC XY: 1940 AN XY: 74492

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.0257

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.00775

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0214 Hom.: 5

Bravo AF: 0.0292

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806237; hg19: chr1-100715782;