rs7720838

chr5-40486794-G-T

Variant summary

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

The ENST00000648975.1(ENSG00000285616):n.2420+1217C>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 0.508 in 151,870 control chromosomes in the GnomAD database, including 20,417 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 0.51 (20417 hom., cov: 31)
• Consequence: ENST00000648975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648975.1	n.2420+1217C>A		intron_variant, non_coding_transcript_variant
	ENST00000649444.1	n.242+296G>T		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.120-17077G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77124 AN: 151752 Hom.: 20399 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.508 AC: 77175 AN: 151870 Hom.: 20417 Cov.: 31 AF XY: 0.498 AC XY: 36920 AN XY: 74210

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.498

Alfa AF: 0.556 Hom.: 49553

Bravo AF: 0.510

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.71
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7720838; hg19: chr5-40486896;