rs1362212

Variant names:

• chr7-35265695-G-A
• rs1362212

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 152,198 control chromosomes in the GnomAD database, including 1,219 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 (1219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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: 16921 AN: 152078 Hom.: 1219 Cov.: 32

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.111 AC: 16918 AN: 152198 Hom.: 1219 Cov.: 32 AF XY: 0.106 AC XY: 7883 AN XY: 74420

African (AFR) AF: 0.0416 AC: 1726 AN: 41528

American (AMR) AF: 0.125 AC: 1910 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3472

East Asian (EAS) AF: 0.0795 AC: 412 AN: 5182

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4822

European-Finnish (FIN) AF: 0.0589 AC: 624 AN: 10596

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10583 AN: 68008

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.146 Hom.: 5194

Bravo AF: 0.115

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.44
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1362212; hg19: chr7-35305306;