rs1077471

Variant names:

• chr17-78329469-T-C
• rs1077471
• ENST00000586321.1:n.60+13681T>C

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.60+13681T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 152,298 control chromosomes in the GnomAD database, including 246 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 0.036 (246 hom., cov: 32)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 0 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371912	NR_188632.1		n.73+13681T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000586321.1	TSL:3	n.60+13681T>C		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.38+13681T>C		intron	N/A
	ENSG00000267737	ENST00000823931.1		n.71+11481T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0365 AC: 5551 AN: 152178 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.00889

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00226

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0364 AC: 5547 AN: 152298 Hom.: 246 Cov.: 32 AF XY: 0.0391 AC XY: 2908 AN XY: 74458

African (AFR) AF: 0.0911 AC: 3786 AN: 41550

American (AMR) AF: 0.0139 AC: 212 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3472

East Asian (EAS) AF: 0.152 AC: 786 AN: 5176

South Asian (SAS) AF: 0.00910 AC: 44 AN: 4834

European-Finnish (FIN) AF: 0.0449 AC: 477 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00226 AC: 154 AN: 68020

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0113 Hom.: 14

Bravo AF: 0.0382

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1077471; hg19: chr17-76325550;