rs6871087

Variant names:

• chr5-30899410-A-G
• rs6871087
• ENST00000797583.1:n.249+6049T>C

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.249+6049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,216 control chromosomes in the GnomAD database, including 786 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 0.082 (786 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 2 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000303861	ENST00000797583.1	n.249+6049T>C		intron_variant	Intron 3 of 4
ENSG00000303879	ENST00000797859.1	n.371+3131A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12444 AN: 152100 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0819 AC: 12472 AN: 152216 Hom.: 786 Cov.: 32 AF XY: 0.0793 AC XY: 5902 AN XY: 74432

African (AFR) AF: 0.176 AC: 7326 AN: 41510

American (AMR) AF: 0.0469 AC: 717 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4830

European-Finnish (FIN) AF: 0.0506 AC: 538 AN: 10624

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0504 AC: 3426 AN: 68002

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0619 Hom.: 1363

Bravo AF: 0.0868

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.63
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6871087; hg19: chr5-30899517;