rs1968201

Positions:

• chr7-103166988-A-G

Variant summary

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

The XM_047421168.1(LOC105375434):​c.*1827A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,348 control chromosomes in the GnomAD database, including 461 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 0.069 (461 hom., cov: 32)
• Consequence: LOC105375434 XM_047421168.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

LOC105375434 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375434	XM_047421168.1	c.*1827A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702842.1	n.175+13915A>G		intron_variant, non_coding_transcript_variant
	ENST00000702099.1	n.154+13915A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10438 AN: 152230 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0686 AC: 10445 AN: 152348 Hom.: 461 Cov.: 32 AF XY: 0.0698 AC XY: 5199 AN XY: 74512

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.0654

Alfa AF: 0.0793 Hom.: 137

Bravo AF: 0.0723

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1968201; hg19: chr7-102807435;