rs16891378

Positions:

• chr6-26188636-A-G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+64465A>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 0.147 in 824,180 control chromosomes in the GnomAD database, including 9,487 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 0.15 (1907 hom., cov: 32)
  • Exomes 𝑓: 0.15 (7580 hom.)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707189.1	n.999+64465A>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+30515A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23435 AN: 152160 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.145 AC: 97700 AN: 671902 Hom.: 7580 AF XY: 0.149 AC XY: 51338 AN XY: 345338

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.112

Gnomad4 EAS exome AF: 0.0789

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome AF: 0.154 AC: 23440 AN: 152278 Hom.: 1907 Cov.: 32 AF XY: 0.155 AC XY: 11537 AN XY: 74450

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.166

Alfa AF: 0.147 Hom.: 1719

Bravo AF: 0.152

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16891378; hg19: chr6-26188864;