rs29684

Variant names:

• chr7-41815054-G-A
• rs29684
• ENST00000839902.1:n.453-56954G>A

Variant summary

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

The ENST00000839902.1(ENSG00000309263):​n.453-56954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,066 control chromosomes in the GnomAD database, including 10,087 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 0.34 (10087 hom., cov: 32)
• Consequence: ENSG00000309263 ENST00000839902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 1 publications found

Genes affected

ENSG00000309263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 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
ENSG00000309263	ENST00000839902.1	n.453-56954G>A		intron_variant	Intron 4 of 5
ENSG00000309263	ENST00000839903.1	n.246-56954G>A		intron_variant	Intron 3 of 3
ENSG00000309263	ENST00000839904.1	n.237-56954G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52239 AN: 151948 Hom.: 10074 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.344 AC: 52282 AN: 152066 Hom.: 10087 Cov.: 32 AF XY: 0.345 AC XY: 25676 AN XY: 74318

African (AFR) AF: 0.178 AC: 7405 AN: 41512

American (AMR) AF: 0.344 AC: 5262 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3464

East Asian (EAS) AF: 0.186 AC: 958 AN: 5156

South Asian (SAS) AF: 0.498 AC: 2395 AN: 4812

European-Finnish (FIN) AF: 0.456 AC: 4816 AN: 10556

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28477 AN: 67972

Other (OTH) AF: 0.357 AC: 754 AN: 2112

Alfa AF: 0.382 Hom.: 2594

Bravo AF: 0.324

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs29684; hg19: chr7-41854652;