rs1895493

Positions:

• chr16-79531006-G-C
• chr16-79531006-G-T

Variant summary

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

The XM_024450279.2(MAF):​c.*28+54874C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,278 control chromosomes in the GnomAD database, including 547 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 0.081 (547 hom., cov: 32)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*28+54874C>G		intron_variant
MAF	XR_001751902.3	n.2015+54874C>G		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2015+54874C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12369 AN: 152160 Hom.: 544 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0813 AC: 12377 AN: 152278 Hom.: 547 Cov.: 32 AF XY: 0.0801 AC XY: 5961 AN XY: 74458

Gnomad4 AFR AF: 0.0609

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0386 Hom.: 29

Bravo AF: 0.0811

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1895493; hg19: chr16-79564903;