rs541041

Variant names:

• chr2-21072103-G-A
• rs541041
• XR_007088659.1:n.578+972G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-21072103-G-A
• chr2-21072103-G-C
• chr2-21072103-G-T

Variant summary

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

The XR_007088659.1(LOC124905593):​n.578+972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,890 control chromosomes in the GnomAD database, including 41,451 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 0.72 (41451 hom., cov: 31)
• Consequence: LOC124905593 XR_007088659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

LOC124905593 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905593	XR_007088659.1	n.578+972G>A		intron_variant	Intron 1 of 2
LOC124905593	XR_007088660.1	n.578+972G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109046 AN: 151772 Hom.: 41443 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.718 AC: 109094 AN: 151890 Hom.: 41451 Cov.: 31 AF XY: 0.724 AC XY: 53775 AN XY: 74232

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.727

Alfa AF: 0.807 Hom.: 106311

Bravo AF: 0.704

Asia WGS AF: 0.906 AC: 3146 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.044
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs541041; hg19: chr2-21294975;