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 ENST00000641494.1(ENSG00000284686):​n.*266+7144G>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: ENSG00000284686 ENST00000641494.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641494.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260971	ENST00000641155.1		n.647-5452G>C		intron	N/A
	ENSG00000260971	ENST00000641302.1		n.322+7144G>C		intron	N/A
	ENSG00000260971	ENST00000641445.1		n.341-5452G>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs778412;

hg19: chr1-56707558;