rs1508212

Positions:

• chr16-65245483-A-G
• chr16-65245483-A-T

Variant summary

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

The ENST00000562656.1(ENSG00000260364):​n.126-6241A>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 0.639 in 152,076 control chromosomes in the GnomAD database, including 31,570 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 0.64 (31570 hom., cov: 33)
• Consequence: ENST00000562656.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903780	XR_007065224.1	n.1138-6241A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562656.1	n.126-6241A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97112 AN: 151958 Hom.: 31551 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.639 AC: 97180 AN: 152076 Hom.: 31570 Cov.: 33 AF XY: 0.629 AC XY: 46727 AN XY: 74336

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.645

Alfa AF: 0.637 Hom.: 61420

Bravo AF: 0.644

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1508212; hg19: chr16-65279386;