rs6816070

Positions:

• chr4-16478734-G-A
• chr4-16478734-G-C

Variant summary

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

The ENST00000512370.5(ENSG00000248138):​n.181-33199G>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 0.637 in 152,032 control chromosomes in the GnomAD database, including 31,627 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 (31627 hom., cov: 33)
• Consequence: ENST00000512370.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

(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 = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374505	XR_007058068.1	n.208+52294G>A		intron_variant, non_coding_transcript_variant
LOC105374505	XR_007058069.1	n.208+52294G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000512370.5	n.181-33199G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96848 AN: 151914 Hom.: 31610 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.637 AC: 96917 AN: 152032 Hom.: 31627 Cov.: 33 AF XY: 0.632 AC XY: 46916 AN XY: 74290

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.635

Alfa AF: 0.602 Hom.: 43161

Bravo AF: 0.648

Asia WGS AF: 0.515 AC: 1791 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	4.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6816070; hg19: chr4-16480357;