rs6670619

chr1-208270177-T-C

Variant summary

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

The ENST00000691549.2(ENSG00000286198):n.467A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,158 control chromosomes in the GnomAD database, including 5,357 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 0.24 (5357 hom., cov: 32)
• Consequence: ENST00000691549.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904501	XR_007066852.1	n.473A>G		non_coding_transcript_exon_variant	1/2
LOC105372889	XR_922508.2	n.357+9402T>C		intron_variant, non_coding_transcript_variant
LOC105372889	XR_922509.2	n.354+9402T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691549.2	n.467A>G		non_coding_transcript_exon_variant	1/2
	ENST00000652300.1	n.491A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37080 AN: 152040 Hom.: 5354 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.244 AC: 37085 AN: 152158 Hom.: 5357 Cov.: 32 AF XY: 0.240 AC XY: 17818 AN XY: 74376

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.255

Alfa AF: 0.289 Hom.: 907

Bravo AF: 0.233

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6670619; hg19: chr1-208443522; COSMIC: COSV60020187;