rs7581129

Positions:

• chr2-4619074-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707165.1(ENSG00000291325):​n.622-8291T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,212 control chromosomes in the GnomAD database, including 749 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 0.087 (749 hom., cov: 33)
• Consequence: ENST00000707165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707165.1	n.622-8291T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13264 AN: 152094 Hom.: 755 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0871 AC: 13261 AN: 152212 Hom.: 749 Cov.: 33 AF XY: 0.0897 AC XY: 6672 AN XY: 74414

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0709 Hom.: 942

Bravo AF: 0.0858

Asia WGS AF: 0.219 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581129; hg19: chr2-4666664;