rs895636

Positions:

• chr2-44961214-C-T

Variant summary

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

The ENST00000425325.2(ENSG00000225156):​n.306C>T 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 0.228 in 152,258 control chromosomes in the GnomAD database, including 4,104 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 0.23 (4100 hom., cov: 31)
  • Exomes 𝑓: 0.17 (4 hom.)
• Consequence: ENSG00000225156 ENST00000425325.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

ENSG00000225156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44961214C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225156	ENST00000425325.2	n.306C>T		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34610 AN: 151864 Hom.: 4095 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.174 AC: 48 AN: 276 Hom.: 4 Cov.: 0 AF XY: 0.160 AC XY: 33 AN XY: 206

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.222

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.228 AC: 34649 AN: 151982 Hom.: 4100 Cov.: 31 AF XY: 0.229 AC XY: 17021 AN XY: 74300

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.221

Alfa AF: 0.203 Hom.: 3544

Bravo AF: 0.233

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs895636; hg19: chr2-45188353;