1-247184887-C-T

Variant names:

• chr1-247184887-C-T
• rs3738443
• ENST00000400933.2:n.596G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400933.2(ENSG00000215795):​n.596G>A 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 0.169 in 589,398 control chromosomes in the GnomAD database, including 10,531 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 0.13 (1717 hom., cov: 32)
  • Exomes 𝑓: 0.18 (8814 hom.)
• Consequence: ENSG00000215795 ENST00000400933.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 12 publications found

Genes affected

ENSG00000215795 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400933.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000215795	ENST00000400933.2	TSL:6	n.596G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305271	ENST00000809956.1		n.734-297C>T		intron	N/A
	ENSG00000305271	ENST00000809957.1		n.714-297C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152098 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.183 AC: 79787 AN: 437182 Hom.: 8814 Cov.: 0 AF XY: 0.197 AC XY: 47813 AN XY: 243088

African (AFR) AF: 0.0293 AC: 377 AN: 12868

American (AMR) AF: 0.107 AC: 3990 AN: 37136

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 2490 AN: 13288

East Asian (EAS) AF: 0.220 AC: 4244 AN: 19266

South Asian (SAS) AF: 0.338 AC: 21264 AN: 62884

European-Finnish (FIN) AF: 0.162 AC: 5727 AN: 35296

Middle Eastern (MID) AF: 0.253 AC: 549 AN: 2166

European-Non Finnish (NFE) AF: 0.162 AC: 37676 AN: 232658

Other (OTH) AF: 0.161 AC: 3470 AN: 21620

GnomAD4 genome AF: 0.132 AC: 20052 AN: 152216 Hom.: 1717 Cov.: 32 AF XY: 0.136 AC XY: 10104 AN XY: 74404

African (AFR) AF: 0.0318 AC: 1321 AN: 41560

American (AMR) AF: 0.122 AC: 1865 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5162

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1840 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11223 AN: 67992

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.140 Hom.: 1571

Bravo AF: 0.122

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs3738443; hg19: chr1-247348189; COSMIC: COSV68931107;