1-67688616-T-C

Variant names:

• chr1-67688616-T-C
• rs606470

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 0.111 in 152,252 control chromosomes in the GnomAD database, including 1,078 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 0.11 (1078 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.111 AC: 16814 AN: 152134 Hom.: 1078 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.111 AC: 16832 AN: 152252 Hom.: 1078 Cov.: 33 AF XY: 0.112 AC XY: 8309 AN XY: 74438

African (AFR) AF: 0.168 AC: 6979 AN: 41562

American (AMR) AF: 0.119 AC: 1817 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3468

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5184

South Asian (SAS) AF: 0.0756 AC: 365 AN: 4828

European-Finnish (FIN) AF: 0.109 AC: 1157 AN: 10590

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5345 AN: 68000

Other (OTH) AF: 0.101 AC: 214 AN: 2116

Alfa AF: 0.0570 Hom.: 83

Bravo AF: 0.115

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.62
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs606470; hg19: chr1-68154299;