rs997493

Positions:

• chr8-60084492-G-A

Variant summary

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

The ENST00000655977.1(ENSG00000254775):​n.360+9769G>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 0.202 in 152,030 control chromosomes in the GnomAD database, including 3,583 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 0.20 (3583 hom., cov: 32)
• Consequence: ENST00000655977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375861	XR_001745714.3	n.632+9769G>A		intron_variant, non_coding_transcript_variant
LOC105375861	XR_007060918.1	n.354+9769G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655977.1	n.360+9769G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30791 AN: 151910 Hom.: 3586 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.202 AC: 30781 AN: 152030 Hom.: 3583 Cov.: 32 AF XY: 0.204 AC XY: 15175 AN XY: 74318

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.232

Alfa AF: 0.219 Hom.: 497

Bravo AF: 0.193

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997493; hg19: chr8-60997051;