rs11743303

Variant names:

• chr5-56564125-A-G
• rs11743303
• ENST00000611197.2:n.98-7938T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-56564125-A-G
• chr5-56564125-A-T

Variant summary

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

The ENST00000611197.2(C5orf67):​n.98-7938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,222 control chromosomes in the GnomAD database, including 3,387 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 0.21 (3387 hom., cov: 32)
• Consequence: C5orf67 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 14 publications found

Genes affected

C5orf67 (HGNC:51252): (chromosome 5 putative open reading frame 67)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.236-7938T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000611197.2	n.98-7938T>C		intron_variant	Intron 1 of 5	5
C5orf67	ENST00000648716.1	n.212-7938T>C		intron_variant	Intron 1 of 5
C5orf67	ENST00000810738.1	n.426+7388T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31727 AN: 152104 Hom.: 3387 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.209 AC: 31747 AN: 152222 Hom.: 3387 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74428

African (AFR) AF: 0.238 AC: 9864 AN: 41530

American (AMR) AF: 0.226 AC: 3452 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3470

East Asian (EAS) AF: 0.111 AC: 577 AN: 5182

South Asian (SAS) AF: 0.164 AC: 794 AN: 4832

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10612

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13797 AN: 67994

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.198 Hom.: 406

Bravo AF: 0.216

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.45
PhyloP100		-0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11743303; hg19: chr5-55859952; COSMIC: COSV71246381;