chr2-188818836-A-T

Position:

• chr2-188818836-A-T

Variant summary

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

The ENST00000431708.1(ENSG00000223523):​n.160+20450T>A 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 0.116 in 152,158 control chromosomes in the GnomAD database, including 1,343 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 0.12 (1343 hom., cov: 32)
• Consequence: ENST00000431708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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
	ENST00000431708.1	n.160+20450T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17641 AN: 152040 Hom.: 1334 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.116 AC: 17683 AN: 152158 Hom.: 1343 Cov.: 32 AF XY: 0.114 AC XY: 8517 AN XY: 74400

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0895

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.104

Alfa AF: 0.106 Hom.: 125

Bravo AF: 0.120

Asia WGS AF: 0.0260 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497682; hg19: chr2-189683562;