ENST00000429636.1:n.196+71621T>C

Variant names:

• chr2-164179099-A-G
• rs17436622
• ENST00000429636.1:n.196+71621T>C

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+71621T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,218 control chromosomes in the GnomAD database, including 2,072 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 0.15 (2072 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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
ENSG00000237844	ENST00000429636.1	n.196+71621T>C		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22143 AN: 152100 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.146 AC: 22153 AN: 152218 Hom.: 2072 Cov.: 32 AF XY: 0.149 AC XY: 11096 AN XY: 74420

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.158

Alfa AF: 0.171 Hom.: 621

Bravo AF: 0.148

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17436622; hg19: chr2-165035609;