rs3856123

Variant names:

• chr1-182787159-A-G
• rs3856123
• ENST00000795607.1:n.645+5658T>C

Variant summary

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

The ENST00000795607.1(ENSG00000303559):​n.645+5658T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,214 control chromosomes in the GnomAD database, including 6,152 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 0.18 (6152 hom., cov: 32)
• Consequence: ENSG00000303559 ENST00000795607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 3 publications found

Genes affected

ENSG00000303559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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
ENSG00000303559	ENST00000795607.1	n.645+5658T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26894 AN: 152096 Hom.: 6120 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.177 AC: 26971 AN: 152214 Hom.: 6152 Cov.: 32 AF XY: 0.173 AC XY: 12902 AN XY: 74424

African (AFR) AF: 0.532 AC: 22060 AN: 41474

American (AMR) AF: 0.0789 AC: 1208 AN: 15306

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

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5182

South Asian (SAS) AF: 0.0954 AC: 460 AN: 4822

European-Finnish (FIN) AF: 0.0210 AC: 223 AN: 10622

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0364 AC: 2478 AN: 68020

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.0609 Hom.: 1970

Bravo AF: 0.196

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.49
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs3856123; hg19: chr1-182756294;