2-126316168-T-C

Variant names:

• chr2-126316168-T-C
• rs11679324
• ENST00000419223.2:n.389+3631T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435352.1(ENSG00000235774):​n.373+3631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,326 control chromosomes in the GnomAD database, including 143 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 0.037 (143 hom., cov: 32)
• Consequence: ENSG00000235774 ENST00000435352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936

Genes affected

ENSG00000235774 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235774	ENST00000419223.2	n.389+3631T>C		intron_variant	Intron 2 of 2	5
ENSG00000235774	ENST00000435352.1	n.373+3631T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5569 AN: 152208 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0366 AC: 5575 AN: 152326 Hom.: 143 Cov.: 32 AF XY: 0.0369 AC XY: 2750 AN XY: 74490

Gnomad4 AFR AF: 0.0590

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00766

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.0308

Gnomad4 OTH AF: 0.0354

Alfa AF: 0.0213 Hom.: 9

Bravo AF: 0.0351

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11679324; hg19: chr2-127073745;