chr4-62217645-C-A

Position:

• chr4-62217645-C-A

Variant summary

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

The ENST00000687436.2(ENSG00000288659):​n.374-2686C>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 0.454 in 151,774 control chromosomes in the GnomAD database, including 17,290 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 0.45 (17290 hom., cov: 32)
• Consequence: ENST00000687436.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927145	XR_938809.3	n.372-2686C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687436.2	n.374-2686C>A		intron_variant, non_coding_transcript_variant
	ENST00000676649.1	n.447-2686C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68901 AN: 151656 Hom.: 17293 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.454 AC: 68900 AN: 151774 Hom.: 17290 Cov.: 32 AF XY: 0.451 AC XY: 33476 AN XY: 74150

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.448

Alfa AF: 0.527 Hom.: 42402

Bravo AF: 0.435

Asia WGS AF: 0.209 AC: 728 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2015977; hg19: chr4-63083363;