rs1577917

Variant names:

• chr6-85982222-C-T
• rs1577917
• ENST00000666191.1:n.333-1147C>T

Variant summary

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

The ENST00000666191.1(ENSG00000288021):​n.333-1147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,114 control chromosomes in the GnomAD database, including 5,060 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 0.23 (5060 hom., cov: 32)
• Consequence: ENSG00000288021 ENST00000666191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 10 publications found

Genes affected

ENSG00000288021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928842	XR_001744239.1	n.1570-11158C>T		intron_variant	Intron 3 of 5
LOC101928842	XR_001744243.1	n.1433-11158C>T		intron_variant	Intron 2 of 4
LOC101928842	XR_002956361.1	n.1992-11158C>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288021	ENST00000666191.1	n.333-1147C>T		intron_variant	Intron 3 of 7
ENSG00000288021	ENST00000755500.1	n.264-11158C>T		intron_variant	Intron 1 of 2
ENSG00000288021	ENST00000755501.1	n.110-11158C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34448 AN: 151996 Hom.: 5061 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.226 AC: 34442 AN: 152114 Hom.: 5060 Cov.: 32 AF XY: 0.225 AC XY: 16746 AN XY: 74320

African (AFR) AF: 0.0551 AC: 2291 AN: 41548

American (AMR) AF: 0.167 AC: 2554 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1787 AN: 5156

South Asian (SAS) AF: 0.155 AC: 749 AN: 4818

European-Finnish (FIN) AF: 0.357 AC: 3775 AN: 10560

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21781 AN: 67964

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.296 Hom.: 12318

Bravo AF: 0.205

Asia WGS AF: 0.227 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1577917; hg19: chr6-86691940;