chr2-62431121-T-C

Variant names:

• chr2-62431121-T-C
• rs7601770
• ENST00000416845.2:n.152+15692T>C

Variant summary

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

The ENST00000416845.2(ENSG00000228541):​n.152+15692T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,840 control chromosomes in the GnomAD database, including 8,489 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 0.32 (8489 hom., cov: 30)
• Consequence: ENSG00000228541 ENST00000416845.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 2 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374764	XR_002959390.2	n.293+68T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228541	ENST00000416845.2	n.152+15692T>C		intron_variant	Intron 1 of 2	3
ENSG00000228541	ENST00000689590.2	n.199-32718T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000807679.1	n.303-10613T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49207 AN: 151722 Hom.: 8492 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.324 AC: 49219 AN: 151840 Hom.: 8489 Cov.: 30 AF XY: 0.314 AC XY: 23285 AN XY: 74194

African (AFR) AF: 0.320 AC: 13253 AN: 41370

American (AMR) AF: 0.251 AC: 3828 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3466

East Asian (EAS) AF: 0.0289 AC: 150 AN: 5186

South Asian (SAS) AF: 0.195 AC: 937 AN: 4810

European-Finnish (FIN) AF: 0.328 AC: 3447 AN: 10512

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25508 AN: 67932

Other (OTH) AF: 0.308 AC: 649 AN: 2108

Alfa AF: 0.342 Hom.: 1464

Bravo AF: 0.315

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7601770; hg19: chr2-62658256;