6-31387042-C-T

Position:

• chr6-31387042-C-T

Variant summary

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

The XR_007059542.1(LOC124901300):​n.75-221C>T 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 0.317 in 151,928 control chromosomes in the GnomAD database, including 8,012 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 0.32 (8012 hom., cov: 32)
• Consequence: LOC124901300 XR_007059542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LOC124901300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901300	XR_007059542.1	n.75-221C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48083 AN: 151810 Hom.: 7998 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.317 AC: 48144 AN: 151928 Hom.: 8012 Cov.: 32 AF XY: 0.321 AC XY: 23856 AN XY: 74254

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.334

Alfa AF: 0.276 Hom.: 11537

Bravo AF: 0.323

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711269; hg19: chr6-31354819;