chr1-100250226-T-C

Variant names:

• chr1-100250226-T-C
• rs3806237
• ENST00000648283.1:n.600T>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000285530 ENST00000648283.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 3 publications found

Genes affected

ENSG00000285530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648283.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285530	ENST00000648283.1		n.600T>C		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AF: 0.0477 AC: 1983 AN: 41558

American (AMR) AF: 0.0257 AC: 393 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.101 AC: 522 AN: 5176

South Asian (SAS) AF: 0.0103 AC: 50 AN: 4832

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10630

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00775 AC: 527 AN: 68028

Other (OTH) AF: 0.0336 AC: 71 AN: 2112

Alfa AF: 0.0151 Hom.: 62

Bravo AF: 0.0292

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		-0.081
PromoterAI		-0.0052	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3806237; hg19: chr1-100715782;