rs1456222

Positions:

• chr3-66934149-A-G
• chr3-66934149-A-T

Variant summary

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

The XR_940939.2(LOC105377144):​n.74+38196T>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 0.626 in 152,020 control chromosomes in the GnomAD database, including 31,534 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 0.63 (31534 hom., cov: 32)
• Consequence: LOC105377144 XR_940939.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

LOC105377144 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377144	XR_940939.2	n.74+38196T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95139 AN: 151902 Hom.: 31503 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.626 AC: 95202 AN: 152020 Hom.: 31534 Cov.: 32 AF XY: 0.630 AC XY: 46808 AN XY: 74306

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.623

Alfa AF: 0.675 Hom.: 6987

Bravo AF: 0.613

Asia WGS AF: 0.835 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456222; hg19: chr3-66984573;