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. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.436 AC: 18061 AN: 41402

American (AMR) AF: 0.715 AC: 10922 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3829 AN: 5168

South Asian (SAS) AF: 0.755 AC: 3638 AN: 4818

European-Finnish (FIN) AF: 0.709 AC: 7484 AN: 10558

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.616 AC: 41894 AN: 67966

Other (OTH) AF: 0.607 AC: 1278 AN: 2104

Alfa AF: 0.607 Hom.: 76957

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
PhyloP100		1.1

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

Other links and lift over

dbSNP: rs555097; hg19: chr11-57162716;