chr1-112708266-T-C

Variant names:

• chr1-112708266-T-C
• rs11102522
• ENST00000606505.5:c.413+2194A>G

Variant summary

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

The ENST00000606505.5(ENSG00000271810):​c.413+2194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,230 control chromosomes in the GnomAD database, including 3,548 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 0.19 (3548 hom., cov: 33)
• Consequence: ENSG00000271810 ENST00000606505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

ENSG00000271810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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
ENSG00000271810	ENST00000606505.5	c.413+2194A>G		intron_variant	Intron 4 of 7	5		ENSP00000476252.1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29007 AN: 152112 Hom.: 3548 Cov.: 33

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.191 AC: 29008 AN: 152230 Hom.: 3548 Cov.: 33 AF XY: 0.200 AC XY: 14922 AN XY: 74432

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.182

Alfa AF: 0.197 Hom.: 3026

Bravo AF: 0.187

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11102522; hg19: chr1-113250888; COSMIC: COSV53517010; COSMIC: COSV53517010;