rs35721

Variant names:

• chr12-100570593-T-G
• rs35721

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 0.437 in 151,970 control chromosomes in the GnomAD database, including 16,642 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 0.44 (16642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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: 0.437 AC: 66341 AN: 151854 Hom.: 16639 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.437 AC: 66353 AN: 151970 Hom.: 16642 Cov.: 32 AF XY: 0.431 AC XY: 32033 AN XY: 74268

African (AFR) AF: 0.204 AC: 8475 AN: 41480

American (AMR) AF: 0.385 AC: 5874 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2257 AN: 4830

European-Finnish (FIN) AF: 0.502 AC: 5278 AN: 10516

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39868 AN: 67950

Other (OTH) AF: 0.459 AC: 967 AN: 2108

Alfa AF: 0.501 Hom.: 2560

Bravo AF: 0.417

Asia WGS AF: 0.324 AC: 1131 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.82
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs35721; hg19: chr12-100964371;