rs7077830

Variant names:

• chr10-46073546-G-C
• rs7077830

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 0.395 in 152,046 control chromosomes in the GnomAD database, including 12,424 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 0.40 (12424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 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: 0.396 AC: 60088 AN: 151928 Hom.: 12417 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.395 AC: 60119 AN: 152046 Hom.: 12424 Cov.: 32 AF XY: 0.399 AC XY: 29660 AN XY: 74338

African (AFR) AF: 0.281 AC: 11675 AN: 41486

American (AMR) AF: 0.390 AC: 5954 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2374 AN: 5170

South Asian (SAS) AF: 0.567 AC: 2730 AN: 4818

European-Finnish (FIN) AF: 0.387 AC: 4081 AN: 10554

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29893 AN: 67970

Other (OTH) AF: 0.428 AC: 904 AN: 2112

Alfa AF: 0.401 Hom.: 1540

Bravo AF: 0.384

Asia WGS AF: 0.502 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.0
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7077830; hg19: chr10-51522276;