chr5-35461098-T-C

Variant names:

• chr5-35461098-T-C
• rs284737
• ENST00000824642.1:n.137-25605T>C

Variant summary

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

The ENST00000824642.1(ENSG00000307231):​n.137-25605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,040 control chromosomes in the GnomAD database, including 25,534 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 0.55 (25534 hom., cov: 32)
• Consequence: ENSG00000307231 ENST00000824642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 2 publications found

Genes affected

ENSG00000307231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824642.1. 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
	ENSG00000307231	ENST00000824642.1		n.137-25605T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82826 AN: 151924 Hom.: 25469 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.546 AC: 82955 AN: 152040 Hom.: 25534 Cov.: 32 AF XY: 0.551 AC XY: 40932 AN XY: 74332

African (AFR) AF: 0.820 AC: 34019 AN: 41508

American (AMR) AF: 0.532 AC: 8123 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1470 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4000 AN: 5162

South Asian (SAS) AF: 0.710 AC: 3422 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4261 AN: 10560

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26050 AN: 67940

Other (OTH) AF: 0.516 AC: 1088 AN: 2108

Alfa AF: 0.469 Hom.: 29708

Bravo AF: 0.562

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs284737; hg19: chr5-35461200;