rs2480008

Variant names:

• chr6-22895200-C-T
• rs2480008
• ENST00000420572.2:n.197+121525G>A

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.197+121525G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,172 control chromosomes in the GnomAD database, including 2,253 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 0.11 (2253 hom., cov: 32)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 1 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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
ENSG00000233358	ENST00000420572.2	n.197+121525G>A		intron_variant	Intron 2 of 2	3
ENSG00000233358	ENST00000797408.1	n.332-34677G>A		intron_variant	Intron 3 of 3
ENSG00000303849	ENST00000797493.1	n.197-15785G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16217 AN: 152054 Hom.: 2237 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.107 AC: 16272 AN: 152172 Hom.: 2253 Cov.: 32 AF XY: 0.104 AC XY: 7756 AN XY: 74414

African (AFR) AF: 0.323 AC: 13396 AN: 41488

American (AMR) AF: 0.0523 AC: 800 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3472

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5178

South Asian (SAS) AF: 0.0628 AC: 303 AN: 4826

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1278 AN: 68000

Other (OTH) AF: 0.0829 AC: 175 AN: 2110

Alfa AF: 0.0808 Hom.: 245

Bravo AF: 0.119

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.7
DANN	Benign	0.90
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2480008; hg19: chr6-22895429;