rs6873705

Variant names:

• chr5-31366437-G-A
• rs6873705
• ENST00000805273.1:n.441+1025G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-31366437-G-A
• chr5-31366437-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000805273.1(ENSG00000304666):​n.441+1025G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,096 control chromosomes in the GnomAD database, including 4,739 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 0.24 (4739 hom., cov: 32)
• Consequence: ENSG00000304666 ENST00000805273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

Genes affected

ENSG00000304666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 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
ENSG00000304666	ENST00000805273.1	n.441+1025G>A		intron_variant	Intron 2 of 2
ENSG00000304666	ENST00000805274.1	n.299+1025G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35963 AN: 151978 Hom.: 4740 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.236 AC: 35963 AN: 152096 Hom.: 4739 Cov.: 32 AF XY: 0.238 AC XY: 17702 AN XY: 74334

African (AFR) AF: 0.133 AC: 5500 AN: 41508

American (AMR) AF: 0.305 AC: 4658 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1244 AN: 5172

South Asian (SAS) AF: 0.193 AC: 928 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3328 AN: 10550

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18593 AN: 67984

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.261 Hom.: 4574

Bravo AF: 0.231

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	13
DANN	Benign	0.56
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6873705; hg19: chr5-31366544;