rs193170

Variant names:

• chr11-72548096-G-A
• rs193170
• ENST00000774587.1:n.177-250C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-72548096-G-A
• chr11-72548096-G-T

Variant summary

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

The ENST00000774587.1(ENSG00000300856):​n.177-250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,090 control chromosomes in the GnomAD database, including 31,563 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 0.64 (31563 hom., cov: 33)
• Consequence: ENSG00000300856 ENST00000774587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 8 publications found

Genes affected

ENSG00000300856 (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 (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300856	ENST00000774587.1	n.177-250C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96865 AN: 151972 Hom.: 31554 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.637 AC: 96912 AN: 152090 Hom.: 31563 Cov.: 33 AF XY: 0.638 AC XY: 47444 AN XY: 74344

African (AFR) AF: 0.492 AC: 20380 AN: 41458

American (AMR) AF: 0.720 AC: 11002 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2390 AN: 3470

East Asian (EAS) AF: 0.644 AC: 3327 AN: 5164

South Asian (SAS) AF: 0.746 AC: 3607 AN: 4832

European-Finnish (FIN) AF: 0.671 AC: 7094 AN: 10568

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46852 AN: 68004

Other (OTH) AF: 0.666 AC: 1405 AN: 2110

Alfa AF: 0.673 Hom.: 92614

Bravo AF: 0.635

Asia WGS AF: 0.699 AC: 2434 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	3.0
DANN	Benign	0.66
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs193170; hg19: chr11-72259140;