1-70628122-C-A

Variant names:

• chr1-70628122-C-A
• rs8179355

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 0.0476 in 152,236 control chromosomes in the GnomAD database, including 313 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 0.048 (313 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.0475 AC: 7222 AN: 152116 Hom.: 306 Cov.: 34

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0476 AC: 7244 AN: 152236 Hom.: 313 Cov.: 34 AF XY: 0.0507 AC XY: 3770 AN XY: 74432

African (AFR) AF: 0.0406 AC: 1685 AN: 41550

American (AMR) AF: 0.0754 AC: 1152 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5166

South Asian (SAS) AF: 0.117 AC: 566 AN: 4822

European-Finnish (FIN) AF: 0.0320 AC: 339 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1950 AN: 68016

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0384 Hom.: 870

Bravo AF: 0.0513

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.6
DANN	Benign	0.95
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs8179355; hg19: chr1-71093805;