6-23135698-T-C

Position:

• chr6-23135698-T-C

Variant summary

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

The XR_926583.3(LOC105374974):​n.218+39556A>G 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 0.441 in 151,812 control chromosomes in the GnomAD database, including 15,451 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 0.44 (15451 hom., cov: 32)
• Consequence: LOC105374974 XR_926583.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

LOC105374974 (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 (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374974	XR_926583.3	n.218+39556A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66811 AN: 151694 Hom.: 15413 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.441 AC: 66898 AN: 151812 Hom.: 15451 Cov.: 32 AF XY: 0.445 AC XY: 33033 AN XY: 74192

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.450

Alfa AF: 0.388 Hom.: 5780

Bravo AF: 0.456

Asia WGS AF: 0.542 AC: 1876 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4626416; hg19: chr6-23135926;