rs16836417

Variant names:

• chr1-238136541-C-A
• rs16836417
• ENST00000780747.1:n.360+19877C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-238136541-C-A
• chr1-238136541-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000780747.1(ENSG00000301680):​n.360+19877C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,304 control chromosomes in the GnomAD database, including 193 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 0.046 (193 hom., cov: 32)
• Consequence: ENSG00000301680 ENST00000780747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 1 publications found

Genes affected

ENSG00000301680 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780747.1. 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
	ENSG00000301680	ENST00000780747.1		n.360+19877C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7044 AN: 152186 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0463 AC: 7052 AN: 152304 Hom.: 193 Cov.: 32 AF XY: 0.0458 AC XY: 3412 AN XY: 74478

African (AFR) AF: 0.0529 AC: 2197 AN: 41560

American (AMR) AF: 0.0313 AC: 479 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 309 AN: 3468

East Asian (EAS) AF: 0.0355 AC: 184 AN: 5188

South Asian (SAS) AF: 0.102 AC: 491 AN: 4826

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10622

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2943 AN: 68034

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0435 Hom.: 282

Bravo AF: 0.0446

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.68
PhyloP100		0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16836417;

hg19: chr1-238299841;

COSMIC: COSV60041963;