rs3807050

chr6-35545149-G-Achr6-35545149-G-C

Variant summary

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

The ENST00000664260.1(ENSG00000228559):n.315-66G>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 0.18 in 152,032 control chromosomes in the GnomAD database, including 2,958 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 0.18 (2953 hom., cov: 29)
  • Exomes 𝑓: 0.24 (5 hom.)
• Consequence: ENST00000664260.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929309	XR_242006.4	n.181+216G>A		intron_variant, non_coding_transcript_variant
LOC101929309	XR_001744104.2	n.182-71G>A		intron_variant, non_coding_transcript_variant
LOC101929309	XR_242007.4	n.182-66G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664260.1	n.315-66G>A		intron_variant, non_coding_transcript_variant
	ENST00000450618.1	n.141-66G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000658088.1	n.96-66G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27295 AN: 151800 Hom.: 2945 Cov.: 29

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.237 AC: 27 AN: 114 Hom.: 5 Cov.: 0 AF XY: 0.243 AC XY: 18 AN XY: 74

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.357

GnomAD4 genome AF: 0.180 AC: 27327 AN: 151918 Hom.: 2953 Cov.: 29 AF XY: 0.181 AC XY: 13434 AN XY: 74212

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0985

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.155

Alfa AF: 0.122 Hom.: 243

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	13
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3807050; hg19: chr6-35512926;