rs1078602

Variant names:

• chr6-88118800-G-A
• rs1078602

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 0.456 in 152,010 control chromosomes in the GnomAD database, including 16,534 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 0.46 (16534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.514 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: 0.456 AC: 69297 AN: 151890 Hom.: 16535 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.456 AC: 69326 AN: 152010 Hom.: 16534 Cov.: 32 AF XY: 0.453 AC XY: 33678 AN XY: 74288

African (AFR) AF: 0.520 AC: 21570 AN: 41476

American (AMR) AF: 0.336 AC: 5126 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.143 AC: 739 AN: 5176

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5778 AN: 10536

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31918 AN: 67954

Other (OTH) AF: 0.414 AC: 875 AN: 2116

Alfa AF: 0.439 Hom.: 6418

Bravo AF: 0.441

Asia WGS AF: 0.276 AC: 958 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	0.66
DANN	Benign	0.56
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1078602; hg19: chr6-88828518;