rs624076

Variant names:

• chr6-83710074-G-A
• rs624076
• NR_136251.1:n.278+355G>A

Variant summary

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

The NR_136251.1(LOC105377879):​n.278+355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,812 control chromosomes in the GnomAD database, including 10,872 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 0.32 (10872 hom., cov: 32)
• Consequence: LOC105377879 NR_136251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

Genes affected

LOC105377879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377879	NR_136251.1	n.278+355G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48365 AN: 151694 Hom.: 10828 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.319 AC: 48463 AN: 151812 Hom.: 10872 Cov.: 32 AF XY: 0.315 AC XY: 23326 AN XY: 74154

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.314

Alfa AF: 0.217 Hom.: 4156

Bravo AF: 0.339

Asia WGS AF: 0.322 AC: 1125 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	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624076; hg19: chr6-84419793; COSMIC: COSV52132688;