rs16843235

chr1-198516564-A-T

Variant summary

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

The ENST00000660823.1(ENSG00000287989):n.327+2987T>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 0.0971 in 152,176 control chromosomes in the GnomAD database, including 924 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 0.097 (924 hom., cov: 31)
• Consequence: ENST00000660823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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 = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371677	XR_922398.3	n.260+2987T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660823.1	n.327+2987T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14748 AN: 152058 Hom.: 921 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.0839

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

GnomAD4 genome AF: 0.0971 AC: 14772 AN: 152176 Hom.: 924 Cov.: 31 AF XY: 0.0975 AC XY: 7256 AN XY: 74406

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0362

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0900 Hom.: 109

Bravo AF: 0.0967

Asia WGS AF: 0.0310 AC: 110 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	4.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16843235; hg19: chr1-198485694;