8-27693205-C-T

Position:

• chr8-27693205-C-T

Variant summary

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

The XR_007060870.1(LOC124901921):​n.57+928G>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 0.175 in 151,810 control chromosomes in the GnomAD database, including 2,891 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 (2891 hom., cov: 32)
• Consequence: LOC124901921 XR_007060870.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

LOC124901921 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901921	XR_007060870.1	n.57+928G>A		intron_variant, non_coding_transcript_variant
SCARA3	XM_017013536.3	c.1370-4987C>T		intron_variant
SCARA3	XM_017013537.2	c.1370-4987C>T		intron_variant
SCARA3	XR_949419.3	n.1774-4987C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26589 AN: 151702 Hom.: 2894 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.175 AC: 26585 AN: 151810 Hom.: 2891 Cov.: 32 AF XY: 0.177 AC XY: 13085 AN XY: 74126

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.215

Alfa AF: 0.226 Hom.: 1750

Bravo AF: 0.170

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439497; hg19: chr8-27550722;