chr2-198767841-G-A

Variant names:

• chr2-198767841-G-A
• rs12617311
• ENST00000440609.1:n.98+4418C>T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+4418C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,784 control chromosomes in the GnomAD database, including 6,607 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 0.28 (6607 hom., cov: 30)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 29 publications found

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+4418C>T		intron_variant	Intron 1 of 3
LOC105373831	XR_923760.2	n.72+4418C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.98+4418C>T		intron_variant	Intron 1 of 2	4
ENSG00000225421	ENST00000748012.1	n.25+4418C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42947 AN: 151666 Hom.: 6606 Cov.: 30

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.283 AC: 42973 AN: 151784 Hom.: 6607 Cov.: 30 AF XY: 0.285 AC XY: 21159 AN XY: 74150

African (AFR) AF: 0.158 AC: 6542 AN: 41428

American (AMR) AF: 0.307 AC: 4677 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2068 AN: 5120

South Asian (SAS) AF: 0.463 AC: 2221 AN: 4796

European-Finnish (FIN) AF: 0.284 AC: 2994 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22191 AN: 67886

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.318 Hom.: 28012

Bravo AF: 0.281

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12617311; hg19: chr2-199632565;