1-79668438-C-T

Variant names:

• chr1-79668438-C-T
• rs7533906

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 0.271 in 152,102 control chromosomes in the GnomAD database, including 6,109 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 0.27 (6109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.271 AC: 41203 AN: 151984 Hom.: 6096 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.271 AC: 41252 AN: 152102 Hom.: 6109 Cov.: 32 AF XY: 0.280 AC XY: 20838 AN XY: 74332

African (AFR) AF: 0.338 AC: 14033 AN: 41492

American (AMR) AF: 0.325 AC: 4967 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2451 AN: 5158

South Asian (SAS) AF: 0.222 AC: 1073 AN: 4828

European-Finnish (FIN) AF: 0.358 AC: 3784 AN: 10556

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13380 AN: 68008

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.226 Hom.: 12538

Bravo AF: 0.277

Asia WGS AF: 0.345 AC: 1197 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	0.46
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7533906; hg19: chr1-80134123;