rs244040

Variant names:

• chr4-110308365-G-A
• rs244040
• ENST00000833186.1:n.255-41851G>A

Variant summary

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

The ENST00000833186.1(ENSG00000308313):​n.255-41851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,960 control chromosomes in the GnomAD database, including 9,578 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 0.35 (9578 hom., cov: 32)
• Consequence: ENSG00000308313 ENST00000833186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 3 publications found

Genes affected

ENSG00000308313 (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 (SAS) allele frequency at 95% confidence interval = 0.377 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
ENSG00000308313	ENST00000833186.1	n.255-41851G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53185 AN: 151842 Hom.: 9567 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.350 AC: 53213 AN: 151960 Hom.: 9578 Cov.: 32 AF XY: 0.346 AC XY: 25713 AN XY: 74266

African (AFR) AF: 0.361 AC: 14981 AN: 41490

American (AMR) AF: 0.310 AC: 4734 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3468

East Asian (EAS) AF: 0.173 AC: 894 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1880 AN: 4804

European-Finnish (FIN) AF: 0.335 AC: 3517 AN: 10510

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24672 AN: 67960

Other (OTH) AF: 0.375 AC: 790 AN: 2106

Alfa AF: 0.363 Hom.: 11376

Bravo AF: 0.344

Asia WGS AF: 0.303 AC: 1052 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs244040; hg19: chr4-111229521;