chr2-98332937-T-C

Variant names:

• chr2-98332937-T-C
• rs7571001
• ENST00000409490.6:n.398+280A>G

Variant summary

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

The ENST00000409490.6(ENSG00000222000):​n.398+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 ENST00000409490.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 4 publications found

Genes affected

ENSG00000222000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409490.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000222000	ENST00000409490.6	TSL:4	n.398+280A>G		intron	N/A
	ENSG00000222000	ENST00000467398.3	TSL:4	n.546+280A>G		intron	N/A
	ENSG00000222000	ENST00000731073.1		n.282+986A>G		intron	N/A

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

African (AFR) AF: 0.343 AC: 14234 AN: 41472

American (AMR) AF: 0.373 AC: 5698 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.189 AC: 981 AN: 5186

South Asian (SAS) AF: 0.189 AC: 914 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10578

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21088 AN: 67958

Other (OTH) AF: 0.324 AC: 682 AN: 2106

Alfa AF: 0.317 Hom.: 24306

Bravo AF: 0.327

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.51
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7571001; hg19: chr2-98949400;