rs618675

chr1-34684573-T-C

Variant summary

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

The ENST00000666642.1(ENSG00000287703):n.568+592A>G 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 0.23 in 152,082 control chromosomes in the GnomAD database, including 4,289 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 0.23 (4289 hom., cov: 32)
• Consequence: ENST00000666642.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378641	XR_001737964.2	n.155+592A>G		intron_variant, non_coding_transcript_variant
LOC105378641	XR_001737965.2	n.155+592A>G		intron_variant, non_coding_transcript_variant
LOC105378641	XR_001737966.2	n.155+592A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666642.1	n.568+592A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34931 AN: 151962 Hom.: 4275 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.230 AC: 34966 AN: 152082 Hom.: 4289 Cov.: 32 AF XY: 0.231 AC XY: 17204 AN XY: 74334

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.236

Alfa AF: 0.218 Hom.: 1495

Bravo AF: 0.243

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	14
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs618675; hg19: chr1-35150174;