2-105724357-T-C

Variant names:

• chr2-105724357-T-C
• rs10514814
• ENST00000720028.1:n.90+11124A>G

Variant summary

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

The ENST00000720028.1(ENSG00000293937):​n.90+11124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,728 control chromosomes in the GnomAD database, including 3,078 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 0.19 (3078 hom., cov: 29)
• Consequence: ENSG00000293937 ENST00000720028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 4 publications found

Genes affected

ENSG00000293937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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
ENSG00000293937	ENST00000720028.1	n.90+11124A>G		intron_variant	Intron 1 of 1
ENSG00000293937	ENST00000720029.1	n.259+9803A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29514 AN: 151610 Hom.: 3071 Cov.: 29

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.195 AC: 29560 AN: 151728 Hom.: 3078 Cov.: 29 AF XY: 0.198 AC XY: 14670 AN XY: 74118

African (AFR) AF: 0.131 AC: 5438 AN: 41412

American (AMR) AF: 0.265 AC: 4043 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1480 AN: 5088

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4808

European-Finnish (FIN) AF: 0.238 AC: 2501 AN: 10492

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13619 AN: 67904

Other (OTH) AF: 0.208 AC: 436 AN: 2098

Alfa AF: 0.203 Hom.: 5654

Bravo AF: 0.194

Asia WGS AF: 0.246 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.63
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10514814; hg19: chr2-106340814; COSMIC: COSV60088331;