chr2-198640114-G-A

Variant names:

• chr2-198640114-G-A
• rs10497819
• ENST00000440609.1:n.99-60406C>T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.99-60406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 139,598 control chromosomes in the GnomAD database, including 1,969 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 0.10 (1969 hom., cov: 30)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.73-60406C>T		intron_variant	Intron 1 of 3
LOC105373831	XR_923760.2	n.73-60406C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.99-60406C>T		intron_variant	Intron 1 of 2	4
ENSG00000225421	ENST00000829906.1	n.62+8906C>T		intron_variant	Intron 1 of 3
ENSG00000225421	ENST00000829908.1	n.71+8906C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 14113 AN: 139472 Hom.: 1964 Cov.: 30

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0221

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.00375

Gnomad SAS AF: 0.0113

Gnomad FIN AF: 0.00286

Gnomad MID AF: 0.0175

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0782

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

GnomAD4 genome AF: 0.101 AC: 14149 AN: 139598 Hom.: 1969 Cov.: 30 AF XY: 0.0983 AC XY: 6636 AN XY: 67520

African (AFR) AF: 0.316 AC: 12286 AN: 38860

American (AMR) AF: 0.0417 AC: 560 AN: 13442

Ashkenazi Jewish (ASJ) AF: 0.0117 AC: 38 AN: 3250

East Asian (EAS) AF: 0.00376 AC: 17 AN: 4518

South Asian (SAS) AF: 0.0112 AC: 48 AN: 4270

European-Finnish (FIN) AF: 0.00286 AC: 25 AN: 8728

Middle Eastern (MID) AF: 0.0113 AC: 3 AN: 266

European-Non Finnish (NFE) AF: 0.0158 AC: 1003 AN: 63470

Other (OTH) AF: 0.0776 AC: 150 AN: 1934

Alfa AF: 0.0589 Hom.: 327

Bravo AF: 0.106

Asia WGS AF: 0.0230 AC: 78 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.65
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10497819; hg19: chr2-199504838;