rs1159167

chr16-13772557-A-Cchr16-13772557-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000573369.5(ENSG00000262267):n.371+5163T>G variant causes a intron, non coding transcript 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: ENST00000573369.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903645	XR_007064996.1	n.125+5163T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000573369.5	n.371+5163T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000576944.1	n.383+5163T>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.901

Alfa AF: 0.935 Hom.: 86752

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1159167; hg19: chr16-13866414;