rs7727166

chr5-66345342-C-T

Variant summary

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

The ENST00000666197.1(ENSG00000251391):n.382+22360C>T 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 0.275 in 151,872 control chromosomes in the GnomAD database, including 6,180 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 0.27 (6180 hom., cov: 31)
• Consequence: ENST00000666197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 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
	ENST00000666197.1	n.382+22360C>T		intron_variant, non_coding_transcript_variant
	ENST00000663200.1	n.372-20280C>T		intron_variant, non_coding_transcript_variant
	ENST00000665668.1	n.395-20280C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41744 AN: 151756 Hom.: 6181 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.275 AC: 41739 AN: 151872 Hom.: 6180 Cov.: 31 AF XY: 0.279 AC XY: 20715 AN XY: 74152

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.267

Alfa AF: 0.307 Hom.: 15151

Bravo AF: 0.264

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	15
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7727166; hg19: chr5-65641170;