rs1159167

Variant names:

• chr16-13772557-A-C
• rs1159167
• ENST00000573369.5:n.371+5163T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-13772557-A-C
• chr16-13772557-A-T

Variant summary

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

The ENST00000573369.5(ENSG00000262267):​n.371+5163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,058 control chromosomes in the GnomAD database, including 61,247 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 0.89 (61247 hom., cov: 30)
• Consequence: ENSG00000262267 ENST00000573369.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 4 publications found

Genes affected

ENSG00000262267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903645	XR_007064996.1	n.125+5163T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262267	ENST00000573369.5	n.371+5163T>G		intron_variant	Intron 3 of 4	5
ENSG00000262267	ENST00000576944.1	n.383+5163T>G		intron_variant	Intron 3 of 3	4
ENSG00000262267	ENST00000740800.1	n.408+5163T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135873 AN: 151940 Hom.: 61208 Cov.: 30

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.894 AC: 135972 AN: 152058 Hom.: 61247 Cov.: 30 AF XY: 0.897 AC XY: 66690 AN XY: 74330

African (AFR) AF: 0.770 AC: 31888 AN: 41396

American (AMR) AF: 0.935 AC: 14298 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3031 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5165 AN: 5180

South Asian (SAS) AF: 0.948 AC: 4563 AN: 4814

European-Finnish (FIN) AF: 0.946 AC: 10010 AN: 10586

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63974 AN: 68010

Other (OTH) AF: 0.901 AC: 1901 AN: 2110

Alfa AF: 0.930 Hom.: 109122

Bravo AF: 0.890

Asia WGS AF: 0.962 AC: 3334 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.34
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1159167; hg19: chr16-13866414;