6-1524335-G-C

Variant names:

• chr6-1524335-G-C
• rs2569872
• ENST00000808839.1:n.572-4562G>C

Variant summary

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

The ENST00000808839.1(ENSG00000305114):​n.572-4562G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,342 control chromosomes in the GnomAD database, including 567 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 0.084 (567 hom., cov: 32)
• Consequence: ENSG00000305114 ENST00000808839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 5 publications found

Genes affected

ENSG00000305114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723944	XR_427861.4	n.235-21772C>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305114	ENST00000808839.1	n.572-4562G>C		intron_variant	Intron 4 of 4
ENSG00000272279	ENST00000808970.1	n.113-21772C>G		intron_variant	Intron 1 of 2
ENSG00000272279	ENST00000808971.1	n.68-21772C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12809 AN: 152222 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0842 AC: 12822 AN: 152342 Hom.: 567 Cov.: 32 AF XY: 0.0826 AC XY: 6156 AN XY: 74492

African (AFR) AF: 0.0717 AC: 2981 AN: 41576

American (AMR) AF: 0.0689 AC: 1054 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.137 AC: 710 AN: 5178

South Asian (SAS) AF: 0.0592 AC: 286 AN: 4832

European-Finnish (FIN) AF: 0.0616 AC: 654 AN: 10624

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6325 AN: 68032

Other (OTH) AF: 0.0827 AC: 175 AN: 2116

Alfa AF: 0.0313 Hom.: 24

Bravo AF: 0.0860

Asia WGS AF: 0.0880 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.44
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2569872; hg19: chr6-1524570;