rs1357056

Variant names:

• chr6-122042588-A-G
• rs1357056
• ENST00000780095.1:n.460-10420A>G

Variant summary

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

The ENST00000780095.1(ENSG00000289871):​n.460-10420A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,084 control chromosomes in the GnomAD database, including 5,002 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 0.17 (5002 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 6 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780095.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289871	ENST00000780095.1		n.460-10420A>G		intron	N/A
	ENSG00000289871	ENST00000780103.1		n.407-760A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26444 AN: 151966 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.174 AC: 26499 AN: 152084 Hom.: 5002 Cov.: 32 AF XY: 0.169 AC XY: 12563 AN XY: 74340

African (AFR) AF: 0.476 AC: 19725 AN: 41476

American (AMR) AF: 0.0885 AC: 1352 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5158

South Asian (SAS) AF: 0.0430 AC: 207 AN: 4810

European-Finnish (FIN) AF: 0.0458 AC: 486 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4019 AN: 67972

Other (OTH) AF: 0.152 AC: 319 AN: 2104

Alfa AF: 0.111 Hom.: 5410

Bravo AF: 0.191

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.83
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1357056; hg19: chr6-122363734;