rs10505005

Variant names:

• chr8-101004424-C-T
• rs10505005

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 0.214 in 152,074 control chromosomes in the GnomAD database, including 3,783 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 0.21 (3783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 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: 0.214 AC: 32481 AN: 151956 Hom.: 3784 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.214 AC: 32490 AN: 152074 Hom.: 3783 Cov.: 32 AF XY: 0.215 AC XY: 15982 AN XY: 74322

African (AFR) AF: 0.160 AC: 6625 AN: 41502

American (AMR) AF: 0.312 AC: 4770 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3464

East Asian (EAS) AF: 0.0553 AC: 286 AN: 5174

South Asian (SAS) AF: 0.301 AC: 1453 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1580 AN: 10550

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16058 AN: 67978

Other (OTH) AF: 0.219 AC: 463 AN: 2112

Alfa AF: 0.235 Hom.: 2605

Bravo AF: 0.220

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0040
DANN	Benign	0.74
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10505005; hg19: chr8-102016652;