rs7571001

Variant names:

• chr2-98332937-T-C
• rs7571001
• ENST00000409490.5:n.200+280A>G

Variant summary

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

The ENST00000409490.5(ENSG00000222000):​n.200+280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,074 control chromosomes in the GnomAD database, including 7,425 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 0.31 (7425 hom., cov: 32)
• Consequence: ENSG00000222000 ENST00000409490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

ENSG00000222000 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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
ENSG00000222000	ENST00000409490.5	n.200+280A>G		intron_variant	Intron 3 of 3	4
ENSG00000222000	ENST00000467398.2	n.546+280A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46632 AN: 151956 Hom.: 7402 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.307 AC: 46718 AN: 152074 Hom.: 7425 Cov.: 32 AF XY: 0.300 AC XY: 22313 AN XY: 74364

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.324

Alfa AF: 0.313 Hom.: 15511

Bravo AF: 0.327

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7571001; hg19: chr2-98949400;