5-143617086-A-G

Variant names:

• chr5-143617086-A-G
• rs2195262
• ENST00000503323.1:n.104+11355A>G

Variant summary

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

The ENST00000503323.1(ENSG00000249881):​n.104+11355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.98 in 152,278 control chromosomes in the GnomAD database, including 73,157 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 0.98 (73157 hom., cov: 31)
• Consequence: ENSG00000249881 ENST00000503323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 2 publications found

Genes affected

ENSG00000249881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503323.1. 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
	ENSG00000249881	ENST00000503323.1	TSL:3	n.104+11355A>G		intron	N/A
	ENSG00000249881	ENST00000848438.1		n.502+8778A>G		intron	N/A
	ENSG00000249881	ENST00000848439.1		n.187+11355A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149127 AN: 152160 Hom.: 73097 Cov.: 31

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.980 AC: 149246 AN: 152278 Hom.: 73157 Cov.: 31 AF XY: 0.980 AC XY: 72948 AN XY: 74468

African (AFR) AF: 0.994 AC: 41321 AN: 41562

American (AMR) AF: 0.973 AC: 14883 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3359 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5020 AN: 5170

South Asian (SAS) AF: 0.925 AC: 4461 AN: 4824

European-Finnish (FIN) AF: 0.993 AC: 10545 AN: 10618

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66433 AN: 68022

Other (OTH) AF: 0.969 AC: 2040 AN: 2106

Alfa AF: 0.981 Hom.: 9088

Bravo AF: 0.980

Asia WGS AF: 0.938 AC: 3262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2195262; hg19: chr5-142996651;