rs1328950

Variant names:

• chr13-31442143-A-G
• rs1328950
• ENST00000843719.1:n.220-24692A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-31442143-A-G
• chr13-31442143-A-T

Variant summary

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

The ENST00000843719.1(ENSG00000278305):​n.220-24692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,148 control chromosomes in the GnomAD database, including 1,601 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 0.14 (1601 hom., cov: 32)
• Consequence: ENSG00000278305 ENST00000843719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

Genes affected

ENSG00000278305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843719.1. 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
	ENSG00000278305	ENST00000843719.1		n.220-24692A>G		intron	N/A
	ENSG00000278305	ENST00000843720.1		n.487+963A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21505 AN: 152028 Hom.: 1600 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.141 AC: 21520 AN: 152148 Hom.: 1601 Cov.: 32 AF XY: 0.145 AC XY: 10801 AN XY: 74386

African (AFR) AF: 0.125 AC: 5180 AN: 41522

American (AMR) AF: 0.143 AC: 2185 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1386 AN: 5138

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10600

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9121 AN: 67996

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0615 Hom.: 68

Bravo AF: 0.137

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		-0.64

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: rs1328950;

hg19: chr13-32016280;