rs7655182

chr4-87984751-G-Achr4-87984751-G-C

Variant summary

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

The ENST00000662475.1(ENSG00000286618):n.307+4607C>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 0.412 in 151,932 control chromosomes in the GnomAD database, including 13,421 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 0.41 (13421 hom., cov: 32)
• Consequence: ENST00000662475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 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
	ENST00000662475.1	n.307+4607C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62545 AN: 151814 Hom.: 13412 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.412 AC: 62591 AN: 151932 Hom.: 13421 Cov.: 32 AF XY: 0.417 AC XY: 30917 AN XY: 74228

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.389

Alfa AF: 0.386 Hom.: 1962

Bravo AF: 0.414

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7655182; hg19: chr4-88905903;