rs1979406

Variant names:

• chr3-34997830-T-C
• rs1979406
• NR_110817.1:n.207-118364A>G

Variant summary

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

The NR_110817.1(LOC101928135):​n.207-118364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,170 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: LOC101928135 NR_110817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.207-118364A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17840 AN: 152052 Hom.: 1288 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.0985

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.117 AC: 17870 AN: 152170 Hom.: 1288 Cov.: 32 AF XY: 0.116 AC XY: 8638 AN XY: 74396

African (AFR) AF: 0.208 AC: 8646 AN: 41492

American (AMR) AF: 0.0813 AC: 1243 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 199 AN: 3468

East Asian (EAS) AF: 0.0983 AC: 510 AN: 5186

South Asian (SAS) AF: 0.0981 AC: 473 AN: 4822

European-Finnish (FIN) AF: 0.0756 AC: 801 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5673 AN: 68002

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.104 Hom.: 144

Bravo AF: 0.123

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1979406; hg19: chr3-35039322;