chr2-44961214-C-T

Variant names:

• chr2-44961214-C-T
• rs895636
• ENST00000425325.2:n.306C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

Genes affected

ENSG00000225156 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425325.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225156	ENST00000425325.2	TSL:3	n.306C>T		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000225156	ENST00000760330.1		n.136-5204C>T		intron	N/A
	ENSG00000225156	ENST00000760331.1		n.130-5204C>T		intron	N/A

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

African (AFR) AF: 0.250 AC: 2 AN: 8

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.250 AC: 2 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.222 AC: 4 AN: 18

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.148 AC: 32 AN: 216

Other (OTH) AF: 0.375 AC: 6 AN: 16

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

African (AFR) AF: 0.268 AC: 11126 AN: 41458

American (AMR) AF: 0.231 AC: 3528 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2167 AN: 5132

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4806

European-Finnish (FIN) AF: 0.181 AC: 1910 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13193 AN: 67972

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.210 Hom.: 10784

Bravo AF: 0.233

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs895636; hg19: chr2-45188353;