chr1-214265985-A-C

Position:

• chr1-214265985-A-C

Variant summary

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

The XR_007066876.1(LOC124904509):​n.2324-3021T>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 0.931 in 152,294 control chromosomes in the GnomAD database, including 66,345 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 0.93 (66345 hom., cov: 33)
• Consequence: LOC124904509 XR_007066876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

LOC124904509 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904509	XR_007066876.1	n.2324-3021T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141617 AN: 152176 Hom.: 66291 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.931 AC: 141727 AN: 152294 Hom.: 66345 Cov.: 33 AF XY: 0.926 AC XY: 68957 AN XY: 74464

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.907

Alfa AF: 0.929 Hom.: 24458

Bravo AF: 0.921

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
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: rs766499; hg19: chr1-214439328;