rs7546055

Variant names:

• chr1-67693268-A-C
• rs7546055
• ENST00000833641.1:n.297+882T>G

Variant summary

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

The ENST00000833641.1(ENSG00000308370):​n.297+882T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,126 control chromosomes in the GnomAD database, including 7,874 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 0.30 (7874 hom., cov: 33)
• Consequence: ENSG00000308370 ENST00000833641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 5 publications found

Genes affected

ENSG00000308370 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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
ENSG00000308370	ENST00000833641.1	n.297+882T>G		intron_variant	Intron 2 of 2
ENSG00000308370	ENST00000833642.1	n.*35T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44976 AN: 152006 Hom.: 7866 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.296 AC: 45025 AN: 152126 Hom.: 7874 Cov.: 33 AF XY: 0.294 AC XY: 21878 AN XY: 74382

African (AFR) AF: 0.492 AC: 20407 AN: 41474

American (AMR) AF: 0.196 AC: 2998 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.0739 AC: 383 AN: 5182

South Asian (SAS) AF: 0.159 AC: 770 AN: 4828

European-Finnish (FIN) AF: 0.302 AC: 3188 AN: 10570

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15972 AN: 67994

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.248 Hom.: 6278

Bravo AF: 0.295

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs7546055; hg19: chr1-68158951;