rs4374821

Positions:

• chr6-47387757-G-A
• chr6-47387757-G-C
• chr6-47387757-G-T

Variant summary

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

The ENST00000663906.1(ENSG00000287485):​n.417+7669C>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 0.106 in 150,878 control chromosomes in the GnomAD database, including 1,978 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 0.11 (1978 hom., cov: 32)
• Consequence: ENST00000663906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375082	XR_926865.4	n.417+7669C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663906.1	n.417+7669C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16023 AN: 150758 Hom.: 1975 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.00996

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.106 AC: 16032 AN: 150878 Hom.: 1978 Cov.: 32 AF XY: 0.111 AC XY: 8205 AN XY: 73726

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0547

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0808 Hom.: 258

Bravo AF: 0.124

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4374821; hg19: chr6-47355493;