rs16851585

Positions:

• chr1-177599664-C-G

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.336-22714G>C 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 0.135 in 152,124 control chromosomes in the GnomAD database, including 1,663 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 0.14 (1663 hom., cov: 33)
• Consequence: ENST00000664407.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664407.1	n.336-22714G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20571 AN: 152004 Hom.: 1667 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.135 AC: 20574 AN: 152124 Hom.: 1663 Cov.: 33 AF XY: 0.141 AC XY: 10491 AN XY: 74362

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.130

Alfa AF: 0.126 Hom.: 163

Bravo AF: 0.134

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16851585; hg19: chr1-177568799;