1-177528313-T-A

Variant names:

• chr1-177528313-T-A
• rs6425430
• ENST00000438575.7:n.388+45415A>T

Variant summary

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

The ENST00000438575.7(ENSG00000227579):​n.388+45415A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,474 control chromosomes in the GnomAD database, including 20,913 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 0.51 (20913 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000438575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 0 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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
ENSG00000227579	ENST00000438575.7	n.388+45415A>T		intron_variant	Intron 3 of 3	3
ENSG00000227579	ENST00000458070.1	n.436+45415A>T		intron_variant	Intron 3 of 3	5
ENSG00000227579	ENST00000654501.1	n.195+28173A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77845 AN: 151356 Hom.: 20872 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.515 AC: 77946 AN: 151474 Hom.: 20913 Cov.: 32 AF XY: 0.515 AC XY: 38118 AN XY: 73992

African (AFR) AF: 0.673 AC: 27784 AN: 41280

American (AMR) AF: 0.499 AC: 7591 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1501 AN: 3462

East Asian (EAS) AF: 0.594 AC: 3037 AN: 5110

South Asian (SAS) AF: 0.500 AC: 2399 AN: 4802

European-Finnish (FIN) AF: 0.453 AC: 4754 AN: 10486

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29270 AN: 67830

Other (OTH) AF: 0.502 AC: 1057 AN: 2106

Alfa AF: 0.486 Hom.: 2306

Bravo AF: 0.525

Asia WGS AF: 0.563 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.021
DANN	Benign	0.71
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6425430; hg19: chr1-177497448;