rs6427595

Positions:

• chr1-161493708-G-A
• chr1-161493708-G-T

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+89G>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 0.738 in 152,146 control chromosomes in the GnomAD database, including 42,246 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 0.74 (42246 hom., cov: 32)
• Consequence: LOC105371473 XR_922214.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371473	XR_922214.3	n.1903+89G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112180 AN: 152026 Hom.: 42219 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112264 AN: 152146 Hom.: 42246 Cov.: 32 AF XY: 0.733 AC XY: 54464 AN XY: 74352

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.730

Alfa AF: 0.710 Hom.: 4817

Bravo AF: 0.746

Asia WGS AF: 0.454 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6427595; hg19: chr1-161463498;