chr6-27217885-T-C

Position:

• chr6-27217885-T-C

Variant summary

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

The XR_007059536.1(LOC124901293):​n.203+17T>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 0.0846 in 152,178 control chromosomes in the GnomAD database, including 644 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 0.085 (644 hom., cov: 32)
• Consequence: LOC124901293 XR_007059536.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

LOC124901293 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901293	XR_007059536.1	n.203+17T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12867 AN: 152060 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0846 AC: 12871 AN: 152178 Hom.: 644 Cov.: 32 AF XY: 0.0799 AC XY: 5945 AN XY: 74412

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0994 Hom.: 1119

Bravo AF: 0.0826

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13219354; hg19: chr6-27185664;