rs4404878

Variant names:

• chr8-127786148-T-C
• rs4404878

Your query was ambiguous. Multiple possible variants found:

• chr8-127786148-T-C
• chr8-127786148-T-G

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 0.357 in 152,094 control chromosomes in the GnomAD database, including 11,162 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 0.36 (11162 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 7 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 (NFE) 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: 0.357 AC: 54301 AN: 151976 Hom.: 11145 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.357 AC: 54354 AN: 152094 Hom.: 11162 Cov.: 33 AF XY: 0.356 AC XY: 26453 AN XY: 74330

African (AFR) AF: 0.162 AC: 6713 AN: 41488

American (AMR) AF: 0.379 AC: 5787 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1168 AN: 5192

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4820

European-Finnish (FIN) AF: 0.458 AC: 4834 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31170 AN: 67976

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.432 Hom.: 27644

Bravo AF: 0.345

Asia WGS AF: 0.313 AC: 1092 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	1.8
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs4404878; hg19: chr8-128798394;