6-148020622-A-G

Position:

• chr6-148020622-A-G

Variant summary

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

The XR_007059804.1(LOC124901423):​n.16475A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,206 control chromosomes in the GnomAD database, including 54,074 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 0.84 (54074 hom., cov: 32)
• Consequence: LOC124901423 XR_007059804.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

Genes affected

LOC124901423 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901423	XR_007059804.1	n.16475A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422023.1	n.139+214T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127808 AN: 152088 Hom.: 54043 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.840 AC: 127893 AN: 152206 Hom.: 54074 Cov.: 32 AF XY: 0.835 AC XY: 62154 AN XY: 74398

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.836

Alfa AF: 0.867 Hom.: 128929

Bravo AF: 0.822

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1881826; hg19: chr6-148341758;