rs7749823

Variant names:

• chr6-26157851-A-C
• rs7749823
• ENST00000687674.2:n.41T>G

Variant summary

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

The ENST00000687674.2(ENSG00000289117):​n.41T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,208 control chromosomes in the GnomAD database, including 988 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 0.11 (988 hom., cov: 32)
• Consequence: ENSG00000289117 ENST00000687674.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

Genes affected

ENSG00000289117 (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 (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289117	ENST00000687674.2	n.41T>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000291338	ENST00000707191.1	n.730A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000291336	ENST00000707189.1	n.999+33680A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16562 AN: 152090 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.109 AC: 16569 AN: 152208 Hom.: 988 Cov.: 32 AF XY: 0.104 AC XY: 7708 AN XY: 74412

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.118

Alfa AF: 0.121 Hom.: 1135

Bravo AF: 0.115

Asia WGS AF: 0.0520 AC: 180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7749823; hg19: chr6-26158079; COSMIC: COSV56802692;