rs6729545

Positions:

• chr2-48806403-C-A
• chr2-48806403-C-G
• chr2-48806403-C-T

Variant summary

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

The XR_001739460.2(LOC105374594):​n.219-1257C>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 0.344 in 151,992 control chromosomes in the GnomAD database, including 9,574 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 0.34 (9574 hom., cov: 32)
• Consequence: LOC105374594 XR_001739460.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LOC105374594 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374594	XR_001739460.2	n.219-1257C>A		intron_variant, non_coding_transcript_variant
LOC105374594	XR_001739458.1	n.65-1257C>A		intron_variant, non_coding_transcript_variant
LOC105374594	XR_001739459.1	n.140-1257C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52191 AN: 151874 Hom.: 9574 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.344 AC: 52220 AN: 151992 Hom.: 9574 Cov.: 32 AF XY: 0.347 AC XY: 25802 AN XY: 74288

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.335

Alfa AF: 0.317 Hom.: 2084

Bravo AF: 0.335

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729545; hg19: chr2-49033542;