chr2-136248628-C-T

Variant names:

• chr2-136248628-C-T
• rs6430612
• ENST00000837573.1:n.120+2103C>T

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.120+2103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,898 control chromosomes in the GnomAD database, including 16,452 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 0.43 (16452 hom., cov: 31)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 15 publications found

Genes affected

ENSG00000308974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837573.1. 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
	ENSG00000308974	ENST00000837573.1		n.120+2103C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65237 AN: 151780 Hom.: 16455 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.430 AC: 65249 AN: 151898 Hom.: 16452 Cov.: 31 AF XY: 0.419 AC XY: 31116 AN XY: 74240

African (AFR) AF: 0.306 AC: 12683 AN: 41416

American (AMR) AF: 0.267 AC: 4076 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.0528 AC: 273 AN: 5174

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6500 AN: 10508

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38699 AN: 67932

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.474 Hom.: 45920

Bravo AF: 0.397

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6430612; hg19: chr2-137006198;