rs6505228

Variant names:

• chr17-31048159-A-G
• rs6505228
• ENST00000579164.6:n.1140-452T>C

Variant summary

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

The ENST00000579164.6(ENSG00000265798):​n.1140-452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,172 control chromosomes in the GnomAD database, including 8,886 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 (8886 hom., cov: 32)
• Consequence: ENSG00000265798 ENST00000579164.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 4 publications found

Genes affected

ENSG00000265798 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646030	NR_146737.1	n.464-2878T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265798	ENST00000579164.6	n.1140-452T>C		intron_variant	Intron 1 of 5	6
ENSG00000291063	ENST00000580053.1	n.143+2610A>G		intron_variant	Intron 1 of 3	5
ENSG00000290858	ENST00000581652.1	n.194-2878T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29734 AN: 152054 Hom.: 8858 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.196 AC: 29811 AN: 152172 Hom.: 8886 Cov.: 32 AF XY: 0.191 AC XY: 14184 AN XY: 74410

African (AFR) AF: 0.646 AC: 26787 AN: 41448

American (AMR) AF: 0.0829 AC: 1269 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0234 AC: 81 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4816

European-Finnish (FIN) AF: 0.0166 AC: 176 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0138 AC: 936 AN: 68024

Other (OTH) AF: 0.153 AC: 324 AN: 2116

Alfa AF: 0.0532 Hom.: 2358

Bravo AF: 0.219

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs6505228; hg19: chr17-29375177;