rs35285258

Variant names:

• chr10-6076807-C-T
• rs35285258

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 0.183 in 152,050 control chromosomes in the GnomAD database, including 3,361 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 0.18 (3361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 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: 0.183 AC: 27762 AN: 151932 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.183 AC: 27766 AN: 152050 Hom.: 3361 Cov.: 32 AF XY: 0.178 AC XY: 13244 AN XY: 74314

African (AFR) AF: 0.0510 AC: 2116 AN: 41484

American (AMR) AF: 0.229 AC: 3489 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5186

South Asian (SAS) AF: 0.185 AC: 892 AN: 4816

European-Finnish (FIN) AF: 0.170 AC: 1790 AN: 10550

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17158 AN: 67958

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.193 Hom.: 519

Bravo AF: 0.182

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
DANN	Benign	0.71
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs35285258; hg19: chr10-6118770;