rs673871

Variant names:

• chr5-82912453-G-A
• rs673871
• ENST00000718048.1:n.693-4411C>T

Variant summary

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

The ENST00000718048.1(ENSG00000248112):​n.693-4411C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,194 control chromosomes in the GnomAD database, including 291 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 0.043 (291 hom., cov: 32)
• Consequence: ENSG00000248112 ENST00000718048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

Genes affected

ENSG00000248112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718048.1. 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
	ENSG00000248112	ENST00000718048.1		n.693-4411C>T		intron	N/A
	ENSG00000248112	ENST00000718049.1		n.389-49293C>T		intron	N/A
	ENSG00000248112	ENST00000745102.1		n.233+8509C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6590 AN: 152076 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0433 AC: 6592 AN: 152194 Hom.: 291 Cov.: 32 AF XY: 0.0465 AC XY: 3459 AN XY: 74400

African (AFR) AF: 0.0122 AC: 505 AN: 41528

American (AMR) AF: 0.0410 AC: 626 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1121 AN: 5166

South Asian (SAS) AF: 0.0477 AC: 230 AN: 4826

European-Finnish (FIN) AF: 0.0968 AC: 1023 AN: 10572

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2956 AN: 68030

Other (OTH) AF: 0.0417 AC: 88 AN: 2108

Alfa AF: 0.0448 Hom.: 27

Bravo AF: 0.0381

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.018
DANN	Benign	0.36
PhyloP100		-1.4

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: rs673871;

hg19: chr5-82208272;