5-143617086-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000249881 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000249881	ENST00000503323.1	n.104+11355A>G		intron_variant	Intron 1 of 4	3

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

Gnomad4 AFR AF: 0.994

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.969

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2195262; hg19: chr5-142996651;