3-35355995-A-G

Position:

• chr3-35355995-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.624 in 151,656 control chromosomes in the GnomAD database, including 30,965 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 0.62 (30965 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35355995A>G		intergenic_region
LOC101928135	NR_110817.1	n.152+37877T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94479 AN: 151538 Hom.: 30903 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.624 AC: 94593 AN: 151656 Hom.: 30965 Cov.: 31 AF XY: 0.622 AC XY: 46089 AN XY: 74102

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.633

Alfa AF: 0.553 Hom.: 41462

Bravo AF: 0.645

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2167176; hg19: chr3-35397487;