rs10008078

Variant names:

• chr4-154527401-G-A
• rs10008078

Your query was ambiguous. Multiple possible variants found:

• chr4-154527401-G-A
• chr4-154527401-G-T

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 0.236 in 152,122 control chromosomes in the GnomAD database, including 4,678 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 0.24 (4678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.236 AC: 35828 AN: 152004 Hom.: 4661 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 35885 AN: 152122 Hom.: 4678 Cov.: 32 AF XY: 0.240 AC XY: 17865 AN XY: 74358

African (AFR) AF: 0.258 AC: 10719 AN: 41482

American (AMR) AF: 0.229 AC: 3506 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2844 AN: 5168

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4826

European-Finnish (FIN) AF: 0.258 AC: 2724 AN: 10574

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13527 AN: 67988

Other (OTH) AF: 0.223 AC: 470 AN: 2112

Alfa AF: 0.208 Hom.: 9386

Bravo AF: 0.236

Asia WGS AF: 0.355 AC: 1234 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	5.1
DANN	Benign	0.61
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs10008078; hg19: chr4-155448553;