XR_942986.3:n.482-3796A>C

Variant names:

• chr6-129933816-A-C
• rs10457532
• XR_942986.3:n.482-3796A>C

Variant summary

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

The XR_942986.3(LOC105377999):​n.482-3796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,144 control chromosomes in the GnomAD database, including 3,220 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 0.20 (3220 hom., cov: 32)
• Consequence: LOC105377999 XR_942986.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

LOC105377999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30277 AN: 152026 Hom.: 3216 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.199 AC: 30297 AN: 152144 Hom.: 3220 Cov.: 32 AF XY: 0.195 AC XY: 14484 AN XY: 74382

African (AFR) AF: 0.170 AC: 7070 AN: 41524

American (AMR) AF: 0.179 AC: 2741 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5190

South Asian (SAS) AF: 0.148 AC: 714 AN: 4816

European-Finnish (FIN) AF: 0.172 AC: 1822 AN: 10602

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16412 AN: 67950

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.216 Hom.: 476

Bravo AF: 0.200

Asia WGS AF: 0.0950 AC: 333 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.47
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10457532; hg19: chr6-130254961;