rs624516

Variant names:

• chr16-31976404-C-T
• rs624516
• ENST00000831886.1:n.206G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000831886.1(ENSG00000308135):​n.206G>A 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 0.0065 in 151,490 control chromosomes in the GnomAD database, including 7 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 0.0065 (7 hom., cov: 30)
  • Exomes 𝑓: 0.0056 (28 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000308135 ENST00000831886.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 1 publications found

Genes affected

ENSG00000308135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd4 at 7 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308135	ENST00000831886.1		n.206G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000260628	ENST00000568208.6	TSL:6	n.268-105C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00649 AC: 983 AN: 151374 Hom.: 7 Cov.: 30

Gnomad AFR AF: 0.00362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000973

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00824

Gnomad OTH AF: 0.0144

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00558 AC: 3775 AN: 676828 Hom.: 28 AF XY: 0.00587 AC XY: 2058 AN XY: 350648

African (AFR) AF: 0.00247 AC: 41 AN: 16596

American (AMR) AF: 0.00670 AC: 196 AN: 29238

Ashkenazi Jewish (ASJ) AF: 0.00842 AC: 142 AN: 16874

East Asian (EAS) AF: 0.00183 AC: 59 AN: 32208

South Asian (SAS) AF: 0.00687 AC: 387 AN: 56370

European-Finnish (FIN) AF: 0.000195 AC: 9 AN: 46162

Middle Eastern (MID) AF: 0.0129 AC: 35 AN: 2714

European-Non Finnish (NFE) AF: 0.00598 AC: 2651 AN: 443160

Other (OTH) AF: 0.00761 AC: 255 AN: 33506

GnomAD4 genome AF: 0.00650 AC: 984 AN: 151490 Hom.: 7 Cov.: 30 AF XY: 0.00627 AC XY: 464 AN XY: 74050

African (AFR) AF: 0.00361 AC: 148 AN: 40968

American (AMR) AF: 0.0110 AC: 168 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.000975 AC: 5 AN: 5128

South Asian (SAS) AF: 0.00499 AC: 24 AN: 4812

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10622

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00824 AC: 560 AN: 67938

Other (OTH) AF: 0.0143 AC: 30 AN: 2104

Alfa AF: 0.00539 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs624516; hg19: chr16-31987725;