6-33522105-G-A

Variant names:

• chr6-33522105-G-A
• rs9469457
• XR_001743876.1:n.18-2614C>T

Variant summary

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

The XR_001743876.1(LOC107986537):​n.18-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,224 control chromosomes in the GnomAD database, including 265 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 0.038 (265 hom., cov: 32)
• Consequence: LOC107986537 XR_001743876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

LOC107986537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986537	XR_001743876.1	n.18-2614C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5842 AN: 152106 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00878

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0385 AC: 5858 AN: 152224 Hom.: 265 Cov.: 32 AF XY: 0.0382 AC XY: 2847 AN XY: 74442

African (AFR) AF: 0.110 AC: 4585 AN: 41528

American (AMR) AF: 0.0225 AC: 344 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5174

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4816

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10622

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00878 AC: 597 AN: 68002

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0218 Hom.: 187

Bravo AF: 0.0442

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9469457; hg19: chr6-33489882;