rs1746049

Variant names:

• chr10-44280862-C-T
• rs1746049

Variant summary

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

The variant allele was found at a frequency of 0.223 in 152,058 control chromosomes in the GnomAD database, including 5,578 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 (5578 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33912 AN: 151940 Hom.: 5555 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0334

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.223 AC: 33979 AN: 152058 Hom.: 5578 Cov.: 33 AF XY: 0.220 AC XY: 16390 AN XY: 74340

African (AFR) AF: 0.459 AC: 19035 AN: 41438

American (AMR) AF: 0.131 AC: 2003 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3468

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5174

South Asian (SAS) AF: 0.268 AC: 1293 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10574

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9004 AN: 67978

Other (OTH) AF: 0.219 AC: 461 AN: 2106

Alfa AF: 0.172 Hom.: 4251

Bravo AF: 0.232

Asia WGS AF: 0.182 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1746049; hg19: chr10-44776310;