chr1-56198547-G-A

Variant names:

• chr1-56198547-G-A
• rs778430
• ENST00000641302.1:n.323-14927C>T

Variant summary

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

The ENST00000641302.1(ENSG00000260971):​n.323-14927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,114 control chromosomes in the GnomAD database, including 33,507 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 0.65 (33507 hom., cov: 32)
• Consequence: ENSG00000260971 ENST00000641302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904190	XR_007066111.1	n.197-1187G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260971	ENST00000641302.1	n.323-14927C>T		intron_variant	Intron 2 of 4
ENSG00000260971	ENST00000641348.1	n.303-14927C>T		intron_variant	Intron 2 of 7
ENSG00000284686	ENST00000641494.1	n.*267-14927C>T		intron_variant	Intron 4 of 5			ENSP00000492970.1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99373 AN: 151996 Hom.: 33457 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.654 AC: 99472 AN: 152114 Hom.: 33507 Cov.: 32 AF XY: 0.651 AC XY: 48384 AN XY: 74374

African (AFR) AF: 0.811 AC: 33666 AN: 41522

American (AMR) AF: 0.599 AC: 9144 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2410 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2605 AN: 5164

South Asian (SAS) AF: 0.760 AC: 3664 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5455 AN: 10568

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40418 AN: 67984

Other (OTH) AF: 0.671 AC: 1418 AN: 2112

Alfa AF: 0.633 Hom.: 6713

Bravo AF: 0.662

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs778430; hg19: chr1-56664219;