rs2143823

Positions:

• chr6-77452800-A-G

Variant summary

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

The XM_047419660.1(LOC105377864):​c.-3743+11367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 152,314 control chromosomes in the GnomAD database, including 471 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 0.057 (471 hom., cov: 33)
• Consequence: LOC105377864 XM_047419660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377864	XM_047419660.1	c.-3743+11367A>G		intron_variant			XP_047275616.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8710 AN: 152196 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0572 AC: 8718 AN: 152314 Hom.: 471 Cov.: 33 AF XY: 0.0590 AC XY: 4397 AN XY: 74478

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.0853

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0234

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0409 Hom.: 52

Bravo AF: 0.0664

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143823; hg19: chr6-78162517;