rs305067

Positions:

• chr16-85938234-C-G
• chr16-85938234-C-T

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.78-7182C>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 0.751 in 152,092 control chromosomes in the GnomAD database, including 44,080 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 0.75 (44080 hom., cov: 31)
• Consequence: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646214.1	n.78-7182C>G		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.393+5960C>G		intron_variant, non_coding_transcript_variant
	ENST00000646986.1	n.715+2223C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114121 AN: 151974 Hom.: 44013 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.751 AC: 114255 AN: 152092 Hom.: 44080 Cov.: 31 AF XY: 0.757 AC XY: 56305 AN XY: 74332

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.695

Alfa AF: 0.706 Hom.: 4568

Bravo AF: 0.754

Asia WGS AF: 0.833 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305067; hg19: chr16-85971840;