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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377979	XR_001744323.2	n.900-10420A>G		intron_variant	Intron 6 of 6
LOC105377979	XR_001744324.2	n.900-10420A>G		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289871	ENST00000780095.1	n.460-10420A>G		intron_variant	Intron 4 of 5
ENSG00000289871	ENST00000780103.1	n.407-760A>G		intron_variant	Intron 3 of 3

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 v4.3

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;