chr5-30984192-G-T

Variant names:

• chr5-30984192-G-T
• rs1021711
• ENST00000797583.1:n.71-2809C>A

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.71-2809C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,904 control chromosomes in the GnomAD database, including 15,536 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 0.45 (15536 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 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.71-2809C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68113 AN: 151784 Hom.: 15522 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.449 AC: 68161 AN: 151904 Hom.: 15536 Cov.: 32 AF XY: 0.448 AC XY: 33255 AN XY: 74214

African (AFR) AF: 0.505 AC: 20918 AN: 41426

American (AMR) AF: 0.489 AC: 7463 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2538 AN: 5162

South Asian (SAS) AF: 0.372 AC: 1788 AN: 4812

European-Finnish (FIN) AF: 0.400 AC: 4218 AN: 10534

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28542 AN: 67942

Other (OTH) AF: 0.438 AC: 920 AN: 2102

Alfa AF: 0.425 Hom.: 33667

Bravo AF: 0.463

Asia WGS AF: 0.400 AC: 1392 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.41
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs1021711; hg19: chr5-30984299;