5-57653695-T-C

Variant names:

• chr5-57653695-T-C
• rs854140
• ENST00000661344.3:n.211+2826T>C

Variant summary

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

The ENST00000661344.3(ENSG00000287709):​n.211+2826T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,978 control chromosomes in the GnomAD database, including 35,079 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 0.68 (35079 hom., cov: 31)
• Consequence: ENSG00000287709 ENST00000661344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 publications found

Genes affected

ENSG00000287709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928505	NR_104668.1	n.100+2936T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287709	ENST00000661344.3	n.211+2826T>C		intron_variant	Intron 1 of 2
ENSG00000287709	ENST00000685494.1	n.104+2936T>C		intron_variant	Intron 1 of 2
ENSG00000287709	ENST00000688166.1	n.88+2936T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102786 AN: 151860 Hom.: 35019 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.677 AC: 102916 AN: 151978 Hom.: 35079 Cov.: 31 AF XY: 0.673 AC XY: 49961 AN XY: 74228

African (AFR) AF: 0.727 AC: 30135 AN: 41478

American (AMR) AF: 0.606 AC: 9245 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2469 AN: 5162

South Asian (SAS) AF: 0.626 AC: 3012 AN: 4808

European-Finnish (FIN) AF: 0.673 AC: 7105 AN: 10550

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46550 AN: 67934

Other (OTH) AF: 0.665 AC: 1404 AN: 2112

Alfa AF: 0.677 Hom.: 138603

Bravo AF: 0.674

Asia WGS AF: 0.603 AC: 2094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs854140; hg19: chr5-56949522;