chr4-107571209-C-T

Variant names:

• chr4-107571209-C-T
• rs1355990
• XR_939059.3:n.130+7800G>A

Variant summary

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

The XR_939059.3(LOC105377358):​n.130+7800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,848 control chromosomes in the GnomAD database, including 33,958 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 0.66 (33958 hom., cov: 31)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

LOC105377358 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377358	XR_939059.3	n.130+7800G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100870 AN: 151730 Hom.: 33911 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.665 AC: 100968 AN: 151848 Hom.: 33958 Cov.: 31 AF XY: 0.661 AC XY: 49052 AN XY: 74222

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.657

Alfa AF: 0.645 Hom.: 9572

Bravo AF: 0.671

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
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: rs1355990; hg19: chr4-108492366;