rs2928445

Variant names:

• chr10-57387016-T-C
• rs2928445
• ENST00000812047.1:n.75+20221A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-57387016-T-C
• chr10-57387016-T-G

Variant summary

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

The ENST00000812047.1(ENSG00000305625):​n.75+20221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,904 control chromosomes in the GnomAD database, including 5,979 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 0.22 (5979 hom., cov: 29)
• Consequence: ENSG00000305625 ENST00000812047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 4 publications found

Genes affected

ENSG00000305625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1	n.63-10910A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305625	ENST00000812047.1	n.75+20221A>G		intron_variant	Intron 2 of 2
ENSG00000305625	ENST00000812048.1	n.63-10910A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33221 AN: 151786 Hom.: 5972 Cov.: 29

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33273 AN: 151904 Hom.: 5979 Cov.: 29 AF XY: 0.220 AC XY: 16371 AN XY: 74252

African (AFR) AF: 0.482 AC: 19912 AN: 41344

American (AMR) AF: 0.262 AC: 3997 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4810

European-Finnish (FIN) AF: 0.0643 AC: 681 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5628 AN: 67968

Other (OTH) AF: 0.192 AC: 406 AN: 2116

Alfa AF: 0.134 Hom.: 2954

Bravo AF: 0.245

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.76
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2928445; hg19: chr10-59146776;