rs778412

Variant names:

• chr1-56241886-C-G
• rs778412
• ENST00000641155.1:n.647-5452G>C

Variant summary

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

The ENST00000641155.1(ENSG00000260971):​n.647-5452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,918 control chromosomes in the GnomAD database, including 13,462 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 0.41 (13462 hom., cov: 32)
• Consequence: ENSG00000260971 ENST00000641155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

Genes affected

ENSG00000260971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904186	XR_007066107.1	n.14344-5452G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260971	ENST00000641155.1	n.647-5452G>C		intron_variant	Intron 2 of 2
ENSG00000260971	ENST00000641302.1	n.322+7144G>C		intron_variant	Intron 2 of 4
ENSG00000260971	ENST00000641445.1	n.341-5452G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62388 AN: 151800 Hom.: 13445 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.411 AC: 62453 AN: 151918 Hom.: 13462 Cov.: 32 AF XY: 0.410 AC XY: 30468 AN XY: 74240

African (AFR) AF: 0.526 AC: 21810 AN: 41436

American (AMR) AF: 0.384 AC: 5859 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1645 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1772 AN: 5164

South Asian (SAS) AF: 0.557 AC: 2683 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3170 AN: 10512

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24143 AN: 67960

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.384 Hom.: 1438

Bravo AF: 0.418

Asia WGS AF: 0.476 AC: 1656 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs778412; hg19: chr1-56707558;