2-164106976-T-C

Variant summary

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

The ENST00000429636.1(ENSG00000237844):n.196+143744A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,988 control chromosomes in the GnomAD database, including 15,346 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 0.41 (15346 hom., cov: 31)
• Consequence: ENST00000429636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429636.1	n.196+143744A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61779 AN: 151870 Hom.: 15351 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.406 AC: 61772 AN: 151988 Hom.: 15346 Cov.: 31 AF XY: 0.412 AC XY: 30585 AN XY: 74280

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.399

Alfa AF: 0.503 Hom.: 7993

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446468; hg19: chr2-164963486;