chr5-111079903-G-T

Variant names:

• chr5-111079903-G-T
• rs6886755
• ENST00000507269.3:n.213-2427C>A

Variant summary

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

The ENST00000741219.1(ENSG00000253613):​n.137-2858C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,222 control chromosomes in the GnomAD database, including 138 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 0.027 (138 hom., cov: 32)
• Consequence: ENSG00000253613 ENST00000741219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741219.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253613	ENST00000507269.3	TSL:5	n.213-2427C>A		intron	N/A
	ENSG00000253613	ENST00000741219.1		n.137-2858C>A		intron	N/A
	ENSG00000253613	ENST00000741220.1		n.137-3519C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4150 AN: 152104 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000676

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0274 AC: 4171 AN: 152222 Hom.: 138 Cov.: 32 AF XY: 0.0280 AC XY: 2082 AN XY: 74408

African (AFR) AF: 0.0740 AC: 3073 AN: 41530

American (AMR) AF: 0.0371 AC: 568 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.0715 AC: 370 AN: 5178

South Asian (SAS) AF: 0.00789 AC: 38 AN: 4814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.000676 AC: 46 AN: 68006

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0108 Hom.: 72

Bravo AF: 0.0327

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6886755; hg19: chr5-110415601;