rs6556416

Positions:

• chr5-159391737-A-C
• chr5-159391737-A-G
• chr5-159391737-A-T

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.283-796A>C 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 0.755 in 151,874 control chromosomes in the GnomAD database, including 43,557 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 0.75 (43557 hom., cov: 31)
• Consequence: ENST00000635333.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635333.1	n.283-796A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.533-24787A>C		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.54-24787A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114471 AN: 151758 Hom.: 43501 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.754 AC: 114589 AN: 151874 Hom.: 43557 Cov.: 31 AF XY: 0.762 AC XY: 56585 AN XY: 74210

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.745

Alfa AF: 0.684 Hom.: 9497

Bravo AF: 0.758

Asia WGS AF: 0.874 AC: 3027 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6556416; hg19: chr5-158818745;