rs17436622

Positions:

• chr2-164179099-A-G

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, non coding transcript 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: ENST00000429636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000429636.1	n.196+71621T>C		intron_variant, non_coding_transcript_variant		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;