chr3-35101019-G-T

Variant names:

• chr3-35101019-G-T
• rs11129640
• NR_110817.1:n.206+205452C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110817.1(LOC101928135):​n.206+205452C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,820 control chromosomes in the GnomAD database, including 4,329 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 (4329 hom., cov: 31)
• Consequence: LOC101928135 NR_110817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 13 publications found

Genes affected

LOC101928135 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.206+205452C>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35632 AN: 151702 Hom.: 4322 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.235 AC: 35663 AN: 151820 Hom.: 4329 Cov.: 31 AF XY: 0.241 AC XY: 17882 AN XY: 74172

African (AFR) AF: 0.219 AC: 9078 AN: 41414

American (AMR) AF: 0.242 AC: 3694 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 643 AN: 3464

East Asian (EAS) AF: 0.276 AC: 1408 AN: 5104

South Asian (SAS) AF: 0.353 AC: 1700 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2848 AN: 10524

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15506 AN: 67934

Other (OTH) AF: 0.216 AC: 454 AN: 2106

Alfa AF: 0.224 Hom.: 18023

Bravo AF: 0.225

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11129640; hg19: chr3-35142511;