rs35610689

Variant names:

• chr7-22734201-A-G
• rs35610689

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 0.226 in 152,104 control chromosomes in the GnomAD database, including 4,145 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 0.23 (4145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 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: 0.226 AC: 34343 AN: 151986 Hom.: 4144 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.226 AC: 34358 AN: 152104 Hom.: 4145 Cov.: 31 AF XY: 0.223 AC XY: 16596 AN XY: 74360

African (AFR) AF: 0.169 AC: 7004 AN: 41486

American (AMR) AF: 0.274 AC: 4185 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3470

East Asian (EAS) AF: 0.0637 AC: 330 AN: 5180

South Asian (SAS) AF: 0.150 AC: 719 AN: 4808

European-Finnish (FIN) AF: 0.223 AC: 2363 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18474 AN: 67980

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.245 Hom.: 3137

Bravo AF: 0.227

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.58
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs35610689; hg19: chr7-22773820;