rs16832963

chr2-190811941-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000676095.2(ENSG00000228509):n.194+3787C>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 0.0086 in 152,264 control chromosomes in the GnomAD database, including 31 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 0.0086 (31 hom., cov: 32)
• Consequence: ENST00000676095.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0086 (1310/152264) while in subpopulation AMR AF= 0.0501 (765/15276). AF 95% confidence interval is 0.0471. There are 31 homozygotes in gnomad4. There are 780 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 32 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000676095.2	n.194+3787C>G		intron_variant, non_coding_transcript_variant
	ENST00000676152.1	n.256-3026C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00860 AC: 1308 AN: 152146 Hom.: 32 Cov.: 32

Gnomad AFR AF: 0.00118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.00717

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

GnomAD4 genome AF: 0.00860 AC: 1310 AN: 152264 Hom.: 31 Cov.: 32 AF XY: 0.0105 AC XY: 780 AN XY: 74458

Gnomad4 AFR AF: 0.00118

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.0479

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.00121

Gnomad4 OTH AF: 0.00710

Alfa AF: 0.00450 Hom.: 3

Bravo AF: 0.0124

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.11
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832963; hg19: chr2-191676667;