1-177528313-T-A

Position:

• chr1-177528313-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664407.1(ENSG00000227579):​n.703+28173A>T variant causes a intron, non coding transcript 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: ENST00000664407.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664407.1	n.703+28173A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.502

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6425430; hg19: chr1-177497448;