rs6454676

Variant names:

• chr6-88167736-G-A
• rs6454676
• ENST00000756364.1:n.128+42139G>A

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.128+42139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,224 control chromosomes in the GnomAD database, including 2,127 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 0.14 (2127 hom., cov: 33)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 11 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298549	ENST00000756364.1	n.128+42139G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21978 AN: 152106 Hom.: 2125 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.144 AC: 21996 AN: 152224 Hom.: 2127 Cov.: 33 AF XY: 0.141 AC XY: 10522 AN XY: 74426

African (AFR) AF: 0.280 AC: 11605 AN: 41508

American (AMR) AF: 0.0918 AC: 1405 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5176

South Asian (SAS) AF: 0.0807 AC: 390 AN: 4832

European-Finnish (FIN) AF: 0.104 AC: 1104 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6732 AN: 68012

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.109 Hom.: 559

Bravo AF: 0.150

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6454676; hg19: chr6-88877455;