rs10497819

chr2-198640114-G-Achr2-198640114-G-T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):n.99-60406C>T variant causes a intron, non coding transcript 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: ENST00000440609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373831	XR_923759.3	n.73-60406C>T		intron_variant, non_coding_transcript_variant
LOC105373831	XR_923760.2	n.73-60406C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440609.1	n.99-60406C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0117

Gnomad4 EAS AF: 0.00376

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00286

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0596 Hom.: 145

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497819; hg19: chr2-199504838;