5-67898641-C-T

Variant names:

• chr5-67898641-C-T
• rs10940138
• ENST00000510621.5:n.57+3903G>A

Variant summary

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

The ENST00000510621.5(ENSG00000250421):​n.57+3903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,832 control chromosomes in the GnomAD database, including 3,472 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 (3472 hom., cov: 30)
• Consequence: ENSG00000250421 ENST00000510621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 5 publications found

Genes affected

ENSG00000250421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250421	ENST00000510621.5	n.57+3903G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31616 AN: 151716 Hom.: 3469 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.208 AC: 31625 AN: 151832 Hom.: 3472 Cov.: 30 AF XY: 0.204 AC XY: 15109 AN XY: 74198

African (AFR) AF: 0.192 AC: 7950 AN: 41370

American (AMR) AF: 0.257 AC: 3915 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3468

East Asian (EAS) AF: 0.147 AC: 757 AN: 5152

South Asian (SAS) AF: 0.146 AC: 704 AN: 4816

European-Finnish (FIN) AF: 0.0964 AC: 1017 AN: 10552

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15214 AN: 67930

Other (OTH) AF: 0.241 AC: 508 AN: 2106

Alfa AF: 0.225 Hom.: 8587

Bravo AF: 0.225

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10940138; hg19: chr5-67194469;