rs1157366

Variant names:

• chr20-7082489-A-C
• rs1157366
• ENST00000425900.1:n.81+12795A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-7082489-A-C
• chr20-7082489-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425900.1(ENSG00000232271):​n.81+12795A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,850 control chromosomes in the GnomAD database, including 5,502 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 0.22 (5502 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 0 publications found

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232271	ENST00000425900.1	TSL:2	n.81+12795A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33855 AN: 151732 Hom.: 5474 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.223 AC: 33938 AN: 151850 Hom.: 5502 Cov.: 32 AF XY: 0.223 AC XY: 16545 AN XY: 74226

African (AFR) AF: 0.458 AC: 18958 AN: 41422

American (AMR) AF: 0.244 AC: 3705 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1087 AN: 5144

South Asian (SAS) AF: 0.0962 AC: 463 AN: 4812

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10586

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7710 AN: 67900

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.123 Hom.: 267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1157366; hg19: chr20-7063136;