rs4713244

Positions:

• chr6-29753369-G-A

Variant summary

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

The ENST00000648999.1(ENSG00000285761):​n.355+442G>A 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 0.199 in 141,098 control chromosomes in the GnomAD database, including 3,031 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 0.20 (3031 hom., cov: 23)
• Consequence: ENST00000648999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
	ENST00000648999.1	n.355+442G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.199 AC: 28120 AN: 140976 Hom.: 3030 Cov.: 23

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.199 AC: 28132 AN: 141098 Hom.: 3031 Cov.: 23 AF XY: 0.198 AC XY: 13522 AN XY: 68384

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.155

Alfa AF: 0.234 Hom.: 5730

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713244; hg19: chr6-29721146;