13-39092096-T-C

Variant names:

• chr13-39092096-T-C
• rs2148418
• ENST00000661973.2:n.3957T>C

Variant summary

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

The ENST00000661973.2(ENSG00000273507):​n.3957T>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 0.365 in 152,048 control chromosomes in the GnomAD database, including 13,627 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 0.36 (13627 hom., cov: 32)
• Consequence: ENSG00000273507 ENST00000661973.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 0 publications found

Genes affected

ENSG00000273507 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661973.2. 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
	ENSG00000273507	ENST00000661973.2		n.3957T>C		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000273507	ENST00000663484.1		n.3753T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000273507	ENST00000614005.1	TSL:3	n.257+38768T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55381 AN: 151930 Hom.: 13595 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.365 AC: 55467 AN: 152048 Hom.: 13627 Cov.: 32 AF XY: 0.364 AC XY: 27079 AN XY: 74358

African (AFR) AF: 0.700 AC: 29029 AN: 41478

American (AMR) AF: 0.306 AC: 4674 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2018 AN: 5148

South Asian (SAS) AF: 0.408 AC: 1967 AN: 4826

European-Finnish (FIN) AF: 0.207 AC: 2186 AN: 10574

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14118 AN: 67966

Other (OTH) AF: 0.306 AC: 646 AN: 2108

Alfa AF: 0.260 Hom.: 3684

Bravo AF: 0.385

Asia WGS AF: 0.409 AC: 1425 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2148418;

hg19: chr13-39666233;