3-35043475-T-C

Variant names:

• chr3-35043475-T-C
• rs713144
• NR_110817.1:n.207-164009A>G

Variant summary

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

The NR_110817.1(LOC101928135):​n.207-164009A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,064 control chromosomes in the GnomAD database, including 15,211 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 0.41 (15211 hom., cov: 32)
• Consequence: LOC101928135 NR_110817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.207-164009A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62896 AN: 151946 Hom.: 15187 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.414 AC: 62972 AN: 152064 Hom.: 15211 Cov.: 32 AF XY: 0.412 AC XY: 30638 AN XY: 74340

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.381

Alfa AF: 0.339 Hom.: 4090

Bravo AF: 0.425

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713144; hg19: chr3-35084967;