rs195371

chr6-37336610-A-Gchr6-37336610-A-T

Variant summary

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

The XR_007059566.1(LOC105375040):n.296-2205T>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 0.332 in 151,624 control chromosomes in the GnomAD database, including 9,500 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 0.33 (9500 hom., cov: 32)
• Consequence: LOC105375040 XR_007059566.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LOC105375040 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375040	XR_007059566.1	n.296-2205T>C		intron_variant, non_coding_transcript_variant
LOC105375040	XR_926762.3	n.296-2205T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50244 AN: 151508 Hom.: 9481 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.332 AC: 50317 AN: 151624 Hom.: 9500 Cov.: 32 AF XY: 0.332 AC XY: 24604 AN XY: 74066

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.324

Alfa AF: 0.264 Hom.: 5203

Bravo AF: 0.343

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195371; hg19: chr6-37304386;