rs4800136

Variant names:

• chr18-22642405-A-C
• rs4800136
• ENST00000716263.1:n.729-29552T>G

Your query was ambiguous. Multiple possible variants found:

• chr18-22642405-A-C
• chr18-22642405-A-G
• chr18-22642405-A-T

Variant summary

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

The ENST00000716263.1(ENSG00000266850):​n.729-29552T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.986 in 152,260 control chromosomes in the GnomAD database, including 74,076 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 0.99 (74076 hom., cov: 31)
• Consequence: ENSG00000266850 ENST00000716263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 2 publications found

Genes affected

ENSG00000266850 (HGNC:58091):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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
ENSG00000266850	ENST00000716263.1	n.729-29552T>G		intron_variant	Intron 5 of 6
ENSG00000266850	ENST00000716264.1	n.924-29552T>G		intron_variant	Intron 7 of 8
ENSG00000266850	ENST00000795021.1	n.678-32212T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.986 AC: 150056 AN: 152142 Hom.: 74032 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.988

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

GnomAD4 genome AF: 0.986 AC: 150159 AN: 152260 Hom.: 74076 Cov.: 31 AF XY: 0.985 AC XY: 73348 AN XY: 74432

African (AFR) AF: 0.969 AC: 40245 AN: 41530

American (AMR) AF: 0.995 AC: 15220 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3422 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4993 AN: 5174

South Asian (SAS) AF: 0.937 AC: 4516 AN: 4820

European-Finnish (FIN) AF: 0.998 AC: 10607 AN: 10624

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67873 AN: 68028

Other (OTH) AF: 0.984 AC: 2082 AN: 2116

Alfa AF: 0.995 Hom.: 90698

Bravo AF: 0.987

Asia WGS AF: 0.941 AC: 3270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.50
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4800136; hg19: chr18-20222368;