1-177332744-C-T

Variant names:

• chr1-177332744-C-T
• rs6660559
• ENST00000811664.1:n.419+1715G>A

Variant summary

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

The ENST00000811664.1(ENSG00000305548):​n.419+1715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,004 control chromosomes in the GnomAD database, including 14,574 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 0.43 (14574 hom., cov: 32)
• Consequence: ENSG00000305548 ENST00000811664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 publications found

Genes affected

ENSG00000305548 (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 (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811664.1. 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
	ENSG00000305548	ENST00000811664.1		n.419+1715G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65807 AN: 151886 Hom.: 14553 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.433 AC: 65864 AN: 152004 Hom.: 14574 Cov.: 32 AF XY: 0.429 AC XY: 31896 AN XY: 74290

African (AFR) AF: 0.361 AC: 14963 AN: 41452

American (AMR) AF: 0.410 AC: 6265 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1201 AN: 3462

East Asian (EAS) AF: 0.487 AC: 2506 AN: 5142

South Asian (SAS) AF: 0.397 AC: 1917 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4870 AN: 10560

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32823 AN: 67962

Other (OTH) AF: 0.413 AC: 871 AN: 2110

Alfa AF: 0.393 Hom.: 1803

Bravo AF: 0.425

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.015
DANN	Benign	0.57
PhyloP100		-1.4

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: rs6660559;

hg19: chr1-177301880;

COSMIC: COSV62372922;