rs4349859

Positions:

• chr6-31398010-G-A
• chr6-31398010-G-C

Variant summary

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

The variant allele was found at a frequency of 0.0306 in 152,092 control chromosomes in the GnomAD database, including 120 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 0.031 (120 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0306 (4650/152092) while in subpopulation NFE AF= 0.0443 (3010/68002). AF 95% confidence interval is 0.0429. There are 120 homozygotes in gnomad4. There are 2342 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 120 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31398010G>A		intergenic_region
MICA-AS1	NR_148222.1	n.417+2044C>T		intron_variant
MICA-AS1	NR_148223.1	n.450+49C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4649 AN: 151974 Hom.: 120 Cov.: 33

Gnomad AFR AF: 0.00740

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0171

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0306 AC: 4650 AN: 152092 Hom.: 120 Cov.: 33 AF XY: 0.0315 AC XY: 2342 AN XY: 74380

Gnomad4 AFR AF: 0.00742

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.0171

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0443

Gnomad4 OTH AF: 0.0190

Alfa AF: 0.0376 Hom.: 184

Bravo AF: 0.0256

Asia WGS AF: 0.0180 AC: 61 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4349859; hg19: chr6-31365787;