rs10056811

Variant names:

• chr5-75309395-G-A
• rs10056811
• XR_007058824.1:n.181+11555C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-75309395-G-A
• chr5-75309395-G-T

Variant summary

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

The XR_007058824.1(LOC124901007):​n.181+11555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,938 control chromosomes in the GnomAD database, including 8,801 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 0.34 (8801 hom., cov: 32)
• Consequence: LOC124901007 XR_007058824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 11 publications found

Genes affected

LOC124901007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901007	XR_007058824.1	n.181+11555C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51304 AN: 151820 Hom.: 8792 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.338 AC: 51330 AN: 151938 Hom.: 8801 Cov.: 32 AF XY: 0.341 AC XY: 25344 AN XY: 74214

African (AFR) AF: 0.298 AC: 12347 AN: 41428

American (AMR) AF: 0.329 AC: 5023 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1588 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1639 AN: 5156

South Asian (SAS) AF: 0.555 AC: 2676 AN: 4818

European-Finnish (FIN) AF: 0.354 AC: 3734 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23185 AN: 67950

Other (OTH) AF: 0.338 AC: 714 AN: 2112

Alfa AF: 0.341 Hom.: 13048

Bravo AF: 0.326

Asia WGS AF: 0.420 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
DANN	Benign	0.72
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10056811; hg19: chr5-74605220;