rs2471042

Variant names:

• chr5-86881956-A-G
• rs2471042
• ENST00000724121.1:n.149+41733T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-86881956-A-G
• chr5-86881956-A-T

Variant summary

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

The ENST00000724121.1(ENSG00000294529):​n.149+41733T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,918 control chromosomes in the GnomAD database, including 36,610 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 0.69 (36610 hom., cov: 30)
• Consequence: ENSG00000294529 ENST00000724121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 5 publications found

Genes affected

ENSG00000294529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) 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
ENSG00000294529	ENST00000724121.1	n.149+41733T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105119 AN: 151798 Hom.: 36578 Cov.: 30

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.693 AC: 105211 AN: 151918 Hom.: 36610 Cov.: 30 AF XY: 0.693 AC XY: 51424 AN XY: 74258

African (AFR) AF: 0.742 AC: 30755 AN: 41440

American (AMR) AF: 0.650 AC: 9927 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2244 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3330 AN: 5126

South Asian (SAS) AF: 0.675 AC: 3244 AN: 4808

European-Finnish (FIN) AF: 0.707 AC: 7458 AN: 10552

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.676 AC: 45926 AN: 67944

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.675 Hom.: 77572

Bravo AF: 0.691

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2471042; hg19: chr5-86177773;