rs224869

Variant names:

• chr5-82448142-A-C
• rs224869
• ENST00000775236.1:n.67+13065A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-82448142-A-C
• chr5-82448142-A-T

Variant summary

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

The ENST00000775236.1(ENSG00000300956):​n.67+13065A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,840 control chromosomes in the GnomAD database, including 11,354 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 0.36 (11354 hom., cov: 31)
• Consequence: ENSG00000300956 ENST00000775236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

ENSG00000300956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775236.1. 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
	ENSG00000300956	ENST00000775236.1		n.67+13065A>C		intron	N/A
	ENSG00000300956	ENST00000775237.1		n.43+13065A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54559 AN: 151722 Hom.: 11358 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.359 AC: 54555 AN: 151840 Hom.: 11354 Cov.: 31 AF XY: 0.364 AC XY: 27003 AN XY: 74188

African (AFR) AF: 0.148 AC: 6116 AN: 41380

American (AMR) AF: 0.321 AC: 4900 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3464

East Asian (EAS) AF: 0.328 AC: 1687 AN: 5150

South Asian (SAS) AF: 0.528 AC: 2535 AN: 4804

European-Finnish (FIN) AF: 0.520 AC: 5475 AN: 10524

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31184 AN: 67942

Other (OTH) AF: 0.354 AC: 746 AN: 2106

Alfa AF: 0.422 Hom.: 63140

Bravo AF: 0.333

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.66
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs224869;

hg19: chr5-81743961;