rs555097

Variant names:

• chr11-57395243-A-C
• rs555097
• ENST00000529411.1:c.304-5287T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-57395243-A-C
• chr11-57395243-A-T

Variant summary

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

The ENST00000529411.1(ENSG00000254979):​c.304-5287T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,970 control chromosomes in the GnomAD database, including 27,626 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 0.59 (27626 hom., cov: 31)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 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
ENSG00000254979	ENST00000529411.1	c.304-5287T>G		intron_variant	Intron 2 of 3	4		ENSP00000431536.1
ENSG00000254979	ENST00000528835.1	n.*213-5287T>G		intron_variant	Intron 1 of 2	3		ENSP00000431480.1
ENSG00000254979	ENST00000534081.5	n.848+4253T>G		intron_variant	Intron 8 of 12	2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90148 AN: 151852 Hom.: 27612 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.594 AC: 90198 AN: 151970 Hom.: 27626 Cov.: 31 AF XY: 0.603 AC XY: 44800 AN XY: 74274

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.607

Alfa AF: 0.617 Hom.: 45293

Bravo AF: 0.587

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.81

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: rs555097; hg19: chr11-57162716;