chr5-162656512-G-A

Position:

• chr5-162656512-G-A

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.1148+3590C>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 0.425 in 151,856 control chromosomes in the GnomAD database, including 14,765 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 0.43 (14765 hom., cov: 31)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377698	XR_001742958.1	n.418+3590C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646617.1	n.1148+3590C>T		intron_variant, non_coding_transcript_variant
	ENST00000644348.1	n.26-32298C>T		intron_variant, non_coding_transcript_variant
	ENST00000660514.1	n.713+3590C>T		intron_variant, non_coding_transcript_variant
	ENST00000663711.1	n.462+3590C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64542 AN: 151738 Hom.: 14743 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.425 AC: 64609 AN: 151856 Hom.: 14765 Cov.: 31 AF XY: 0.411 AC XY: 30538 AN XY: 74212

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.434

Alfa AF: 0.419 Hom.: 18191

Bravo AF: 0.442

Asia WGS AF: 0.189 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.45
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7711337; hg19: chr5-162083518;