1-177652066-T-C

Position:

• chr1-177652066-T-C

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.336-75116A>G 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 0.468 in 152,032 control chromosomes in the GnomAD database, including 17,029 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 0.47 (17029 hom., cov: 32)
• Consequence: ENST00000664407.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 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.336-75116A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71023 AN: 151914 Hom.: 17001 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.468 AC: 71096 AN: 152032 Hom.: 17029 Cov.: 32 AF XY: 0.463 AC XY: 34376 AN XY: 74312

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.485

Alfa AF: 0.501 Hom.: 18398

Bravo AF: 0.465

Asia WGS AF: 0.317 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572511; hg19: chr1-177621201;